Boarding an External Command Seat on the launchpad causes the ship to be removed.

KSP.log output:

[KerbalSeat]: Boarded by Untitled Space Craft
[LOG 19:36:20.952] [1021.669] DarkMultiPlayer: Vessel docking detected!
[LOG 19:36:20.953] [1021.669] DarkMultiPlayer: Inconsistent docking state detected, killing both vessels if possible.
[LOG 19:36:20.954] Untitled Space Craft Unloaded
[LOG 19:36:20.956] Packing Untitled Space Craft for orbit
[LOG 19:36:20.973] Added 0.0001489075 (-10) reputation: 'VesselLoss'.
[LOG 19:36:20.975] [00:00:03]: Billy-Bobbree Kerman was killed.
[LOG 19:36:20.997] [1021.694] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:20.998] [1021.694] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.013] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.035] [1021.739] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.036] [1021.739] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.049] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.061] [1021.777] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.062] [1021.777] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.076] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.091] [1021.803] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.092] [1021.803] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.107] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.123] [1021.833] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.124] [1021.833] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.142] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.159] [1021.866] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.160] [1021.866] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.174] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.195] [1021.901] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.196] [1021.901] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.209] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.222] [1021.937] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.223] [1021.937] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.236] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.249] [1021.964] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.250] [1021.964] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.264] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.281] [1021.991] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.282] [1021.991] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.296] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.310] [1022.023] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.311] [1022.023] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.326] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.339] [1022.052] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.340] [1022.052] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.356] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.369] [1022.081] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.370] [1022.081] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.383] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.400] [1022.111] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.401] [1022.111] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.416] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.430] [1022.142] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.432] [1022.142] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.444] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.455] [1022.173] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.457] [1022.173] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.470] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.483] [1022.198] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.484] [1022.198] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.497] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.511] [1022.225] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.512] [1022.225] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.530] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.542] [1022.254] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.544] [1022.254] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.556] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.576] [1022.285] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.578] [1022.285] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.592] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.605] [1022.32] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.606] [1022.32] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.619] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.634] [1022.347] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.635] [1022.347] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.648] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.660] [1022.376] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.661] [1022.376] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.674] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.687] [1022.402] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.688] [1022.402] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.702] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.716] [1022.429] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.717] [1022.429] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.735] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.747] [1022.459] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.749] [1022.459] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.762] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.778] [1022.49] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.779] [1022.49] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.793] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.806] [1022.521] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.807] [1022.521] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.821] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.836] [1022.549] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.838] [1022.549] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.851] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.863] [1022.579] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.864] [1022.579] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.878] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.893] [1022.605] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.894] [1022.605] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.908] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.
[LOG 19:36:21.923] [1022.635] DarkMultiPlayer: Delay killing 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.925] [1022.635] DarkMultiPlayer: Killing vessel: 8176b451-dfd6-452c-afd7-9ff7d09ae046
[LOG 19:36:21.941] Added 8.775134E-05 (-10) reputation: 'VesselLoss'.

Should be fixed via 0a7bb86 - I've done basic testing but I'll let you close this one if it really is fixed :)

Looks fixed to me. Thanks!