I will not claim to be an expert or an authority on this subject but, relatively recently, I ALSO had to find the answer to this subject and arrived at a conclusion.
X68K roms where Simon is taking ANYTHING different from 2 bars damage in Stage 1, Loop 1, are hacked, and there are numerous ROMs with different damage numbers across different stages. To get to this conclusion, I watched gameplays done on real hardware, and someone on the Shmup forums fired up their own factory-protected copy of the game and also made sure to check that Simon is supposed to take 2 bars damage.
This is what they concluded from playing their copy:Stage 1 = -2 HP
Stage 2 = -3 HP
Stage 3 = -4 HP
Stage 4 = -4 HP
The stage 3 damage count onwards aligns with
this playthrough found on Youtube, which the user claims to have captured on real hardware.
Here's another on NicoNico whose user also claims to have captured on real hardware where the damage on Stage 3 onwards also aligns.
Here's one more video on Youtube where you can see the ACTUAL hardware itself hooked to a TV, and you can see the player taking damage on earlier levels confirming Stage 1, 2 and 3 damage scales.
Again, I'm not an authority and this was kind of a quick research at the time. But this all seems to align with the actual original mode on Castlevania Chronicles. Since I could not confirm if other revisions of the game were released, and since a more recent revision should be the basis for Chronicles' original mode but there seems to be no difference between it and the ones played on real hardware, I concluded those must be romhacks.