As of Reliquary-1.12.2-1.3.4.796, the Ender staff can be used to enter protected area.
Please use the EnderTeleportEvent cancellable event when teleporting player, like Ender pearls, Endermen and Shulkers do.

If this is still an issue than +1 on it being fixed for 1.12.2 if 1.12.2 is still in development.

not for 1.12.2 at this point but this is now added in 1.16.5 dev build and will be released soon

this is now included in the latest release on curseforge