Fellow Kerbonaut DY_ZBX realized something interesting about merging crafts:

I did the following operations.
Re-created and saved both crafts, but still had the same problem as in the video. And I also used Craft Manager at the same time.

When I don't modify the parent part, though, the problem doesn't seem to arise.

Sounds like something missing on AtttachedOnEditor - this may be related with the original problem incepted by ModulePartVariant that was failing to initialise on some circunstaces and was bruteforced on KSP 1.4.3

I think this is a side effect of #66 (being this last one the real issue).

I will try to check this on my next Diagnosing Festival and, if proven true, I will close this one as duplicate as #66 has better Test Sessions.

Addendum! The problem is on rerooting the craft! After rerooting the craft we have the misbehaviour!

If you build the craft in the inverted order, even by "inverting" parts before attachment the problem doesn't happen!