I've been trying to play Zeroigar on an emulator, but I never owned a real PC-FX and don't know what the real display looked like.
Googling shows that it had a resolution of 256x240 or 341.333 (=1024/3) x240. Mednafen when I run it with a scale of 1 claims to be using 288x232 video mode. I ran it with an xscale and yscale of 4 and it has 4x that mode, but it seems to be producing oval planets and oval explosions.
Does Mednafen already scale it properly according to aspect ratio, (so further scaling it by a constant 4 is enough), or do I need to use a different X and Y value to make it look like what people would see on an actual 4:3 TV? Are those planets and explosions supposed to be round?
Zeroigar displays in 256x232 (i.e. 256x240 - 8 lines of overscan).
Well ... there's an exception for one screen, but if you can get your monitor/TV to look right, then Mednafen should take care of it.
AFAIK All that you need to do is to get to any 4:3 output ratio.
BUT ... I've just tested Mednafen in fullscreen mode on my 1920x1080 monitor, and the picture definitely isn't a pure 4:3 ratio, it does look a little "off". I usually play in Windowed-mode and hadn't noticed.
I think that you may need to play with "custom" scalings if you want it to look as-close-as-you're-going-to-get to a real TV.