Surprisingly I haven't run into the boss yet. I'm just mostly doing exploring and crystal collecting. And yes, I know of the lots of enemies on screen case: surprisingly, I have decided to decline to attack any of them and instead just tank and/or avoid the hits. It also means I find the shields to be practical for this scenario.
If you don't want to deal with a missed VBLANK, then I recommend the scanline check approach to avoid that edge case. Either that, or both the SPC700 and SNES-side programming need to be modified to avoid that entirely.