When AutoScaling (CTRL-L on the default settings) parts with multiple bulkheads (as the Kerbodyne S3-S4 Adapter), the auto-scaling is being done in a less than desirable way : since the default scale is the bigger bulkhead, the scaling matches the wrong end of the part to the part being attached.

Of course this will break too when the top end of the part is the bigger bulkhead (inverting the current situation), but this use case is far less common than the current implemented one.

Problem: changing the defaultScale may play havoc with legacy crafts, so this probably should be implemented only on the new Branch of TweakScale, where backwards compatibility is not expected.

After considerations and some toying, I realised that this would not really handle the problem.

By using the smaller part as the default scale, as the OP says, I would just transfer the problem from some parts to others - all I would accomplish is move the problem to a somewhat more uncommon situation.

However, changing the defaultScale is a terribly cumbersome task: it would affects ongoing savegames and current crafts, as the defaultScale is used to recalibrate scalings on loading.

Too much of a hassle for something that would not really fix anything.

A new approach is needed, so I'm closing this one.