CGA emulation has nothing to do with it. Don't mix software and hardware features.
It does actually.
Original IBM VGA is not fully register-compatible with CGA, and it runs the 320x200 mode at 70 Hz instead of 60 Hz.
This makes some games not work properly, and games will just appear in the standard black, cyan, magenta, white palette, because the palette register does not work. It basically only has BIOS-level compatibility with CGA, and even that is limited.
Some VGA clones have a special CGA mode, which you can generally enable with some software tool. This makes them register-compatible, giving you the correct colours. But when connected to a VGA monitor, you're still faced with the 70 Hz issue.
VGA cards that can connect to a 9-pin RGBI CGA/EGA monitor, can do 60 Hz, and therefore could theoretically give 100% compatible CGA mode.