After fiddling around a lot more I managed to get pixel perfect however, it is inconvenient.
Using No change screen resolution fixed aspect full screen I can get pixel perfect, IF I set my computer's screen itself to 1280/800 (multiple of pc98 native screen 640/400)
Changing my screen's resolution back and forth every time I use the emulator is annoying. I also cannot for the life of me find an option to just hard fix a resolution for the emulator to go for.