I miss a more fleshed out controls/gamepad customization screen (the current one is rather too limited) to avoid control issues like the ones you mention, or the ones that also arise in the map screen when remapping the buttons, since the map screen will always keep fixed button associations no matter what.
For example, if you set the speed/run function to the "C" button, since you need to keep pressed "C" in the map screen to allow moving yourself instead of moving the map screen, you will be forced to always run while moving yourself on the map screen. Even though this issue may be solved by simply inverting the "C" button switching logic in the map screen, so you will always move yourself by default and keeping pressed "C" will instead switch to moving the map screen. This would also be more faithful to the map control logic of most of the other versions (not only the PC original is that way, but also others based on the Jaguar version like the original 32X version and the 3DO version), rather than inheriting it straight from the Jaguar version like it is now (it's puzzling why they did that). @Vic speaking about minor fixes, would it be possible to make the game remember the last area you selected when starting a new game during gameplay? So for example, if I'm playing in area 15 and want to go to area 16, it would save from having to manually move the selection from area 1 at all times (or from area 24 backwards which is also another option). Even the faulty 3DO version remembers what was the last area selected/played when the game boots, but it would be enough if this could be done when starting a new game during gameplay and not necessarily after booting the game (even though the SRAM save technically could also remember it), so it would make easier to move between levels from your current one.
Also, I noticed that in the ending, the enemy gallery animations are being played too fast and there's no sound when they fire. I guess those are also issues inherited from the Jaguar version. You already restored their alert sounds and death sounds compared to the Jaguar one, so I wonder if you could also do the same with their fire sounds and also fix the overacceleration they seem to have. Again, even the faulty 3DO version did this right, and the original 32X version also did it almost right too, if it wasn't because for some reason all the death sounds were replaced by shotgun shots.