So, I cheated a new game up to postgame in about 2 hours so I could do some save file analysis.
For whatever reason, it looks like Renko herself is the problem? For all the other characters, there's a distinction between "acquiring through starting an NG+ with all the characters" and "acquiring through their normal events". So even though I start with Minoriko, I still have to "revive" Minoriko to pass by the rock on 5F.
However, for Renko, this seems to not be correctly implemented. It looks like the game does in fact believe I have truly acquired Renko from the start of the game. And it also seems that it will not spawn any of the deformed bosses if Renko is in your party.
This is fixable, to an extent, by doing two things:
1. Removing Renko from your party via PCF01.ngd (set byte 0x2F to 0).
2. Setting offset 0x64A in EVF01.ngd to 1. Or, possibly, clearing the second bit (b & 11111101).
3. It'd be easy to remove the achievements, but I don't know the numbers.
There may be a solution that doesn't require Renko's removal, but I haven't found it. And, in fact, based on the fact that I've never seen anyone else report this issue means it may be more of an edge case than I thought.
Either way, I'm archiving my results here just in case anyone else has this problem.