Hi PhantomP,
For your 1 and 3 issues, there's no software fix. Geometry is problematic on flat tubes due to their own nature. The problem with colors might be caused by your transcoding stack, specially if there's any signal amplification happening.
With regards to your issue 2, you can shift the image up by adding lines to the vertical front porch. Check if you can do it from Arcade OSD itself (keep in mind you can't modify the mode that's currently used by the desktop, either test it on a different mode or switch your desktop mode to something else before attempting a modification.
If this works, then you'll need to port that change to a custom crt_range that can be applied both to VMMaker and GM, so new modes are created that already inherit that change.