I would suggest making individual bugfix patches if possible. Not like separate database entries like FFVI or anything like that, but the thing is that evade and crit in particular tend to change the game a lot more than you'd think. That's one of the reasons why he said the bugfix patch was only being supported for so short; it creates whole other balance issues which Sin of Mana addressed, like OHKOs being everywhere due to enemy crits.
Is it your own experience that those changes hurt the game? I did a complete playthrough of the collection version without bugfixes prior to me being on my 3rd consecutive play of the Corlett version with bugfixes. The original play felt off to me with the damage from attacks always being the same (or to be precise a range of 1 more or 1 less than the standard damage). The variability of adding character and enemy crits created more excitement and never resulted in an excess of character deaths. Honestly, the only thing that has resulted in a lot of character deaths for me is in the last third of the game when enemies start using level 3 techs on your whole party. Crits don't enter into the damage for those at all. Just to mention the fix to evade / accuracy, the impact seemed relatively minor.
As far as me doing fixes separately, I don't have the will or skill to reinvent the wheel here. With those 107 addresses altered by the bugfix patch, I would have no idea which bytes applied to which bugs. I'll be lucky if I can port over the fixes altogether.
I did notice what appears to be a bug that the patch doesn't address. When you go through the God Beast areas, the game has this brilliant mechanic of increasing the enemy levels by 2 or 3 in all the other areas every time you fell a God Beast. However, in Gemstone Valley, about half the enemies don't seem to get this boost and I think they were stuck at 28. The inconsistency here doesn't seem intentional to me.
The original Super Famicom version is a HiROM game while the English "Trials of Mana" is ExHiROM, so that probably has something to do with it.
I have to read more into the differences between HiROM and ExHiROM. But wouldn't the designations for that be in the rom data itself and ultimately convert based on patching the changes between the Japanese rom and the collection rom.