sharing the info i have in hopes we can look further into this
so the MGSMC version of Metal Gear and Metal Gear 2, which is the same version used in MGSHD and MGS3 subsistence, is pretty much an emulator wrapped inside Metal Gear Solid 3. the exact same modified version of Metal Gear was also released through GOG.
i have reasons to believe it's still emulated and not native. exhibit one being the BIOS screen showing up at the beginning.