Yes on the 2 options you outline.
I would expect to see some evidence of balancing on a neutral balanced TC. But if it was one of the few that came out of assembly and just happened to be perfect, then it could not have any marks. I'm just making the observation.... and yes it could be elsewhere. The TC is not hard to pull and re-install... just messy..... You have a lot of unknowns to deal with so I'd not rule out anything.
As for the compression numbers, it sounds like you have tested it well. I just would not expect 150 psi from stock '78 360 pistons, especially if this has any moderately sized cam in it.
Speaking of which, do you have any idea of the cam in this thing?