Is there a simple way to implement this in a custom build?

For some context, I have attempted to make alterations in my own build so that the the line by line drawing method of vgaonly works by default. This does appear to work in VGA modes, as the palette corruption in my test case game, Frontier First Encounters, is gone. However, it seems to make no difference in games that use SVGA modes, assuming that the palette corruption I'm experiencing is caused by mid-frame palette changes (I'm assuming all this, so someone correct me if I'm wrong). Wing Commander 3 is one game affected by this - there are brief bursts of corrupt colours during video sequences (usually when a scene cuts between different cameras). I can mitigate this by running the videos in VGA mode, as they seem to work perfectly in my build, but this is not possible in all games. The 7th Guest is another game that suffers from this, with brief bursts of incorrect colours appearing during transition videos. To be honest, I don't have any retro hardware to test games on any more, but I don't recall this happening when I played them 20 years ago.

Could I have missed something in my alterations, is there a simple way to patch the code to apply to SVGA too, or am I simply barking up the wrong tree? Bear in mind that I'm not enough of a coder to really reverse engineer what's going on on my own.