Hi Jerry.
A variation of this "compound timing" versus "simple timing" problem that Musocity mentions arose earlier this year. In that particular case, it was necessary to consider the 2/3 down-scaling of tempo.
https://www.pgmusic.com/forums/ubbthreads.php?ubb=showflat&Number=735676#Post735676All is fine when everything is done in BIAB because, as you say, BIAB works on musical pulses and 12/8 and 4/4 both have four pulses per bar, and the 12/8 is created as a variation of 4/4. The fact that, in theory, 12/8 has pulses based on dotted quarter notes and 4/4 has pulses based on quarter notes, doesn't cause any conflict.
The problem for the above user arose because of an external MIDI file. I also had a similar problem a couple of years ago when I was trying to match 12/8 EZ Drums to 4/4 (sw) BIAB tracks imported into Reaper. I haven't tried it again since that time so maybe things are now easier.
Regards,
Noel