I did a bunch of hardware testing for flamewing trying different builds to mitigate the CRAM write dots last year, but we never got anywhere really.
The S1 ending dots shouldn't have anything to do with whether you hit the boss or whether explosions appear. Every instance of this is caused by writing to CRAM to change the palette mid-screen: you can see it at the waterline in the original games too, but it's usually masked by some flashing waterline graphics. The save screen is particularly badly affected because it changes palette several times.
Sonic 3 seems to have a way around this, but I don't know exactly how that works. The levels that use it (everything with water apart from HCZ) tend to stutter and occasionally glitch at the moment the waterline scrolls into view, which I assume is related.
The S1 ending dots shouldn't have anything to do with whether you hit the boss or whether explosions appear. Every instance of this is caused by writing to CRAM to change the palette mid-screen: you can see it at the waterline in the original games too, but it's usually masked by some flashing waterline graphics. The save screen is particularly badly affected because it changes palette several times.
Sonic 3 seems to have a way around this, but I don't know exactly how that works. The levels that use it (everything with water apart from HCZ) tend to stutter and occasionally glitch at the moment the waterline scrolls into view, which I assume is related.

