I dont think I have noticed any halved refresh rate issues.
Is there a good example on how to check?
Run a game that requires an interlaced mode, and force -video d3d. You'll notice how the speed is locked at 50%. Pre-169 versions of GM workaround this by forcing -video ddraw but that was always a temporary hack. Version 169 no longer requires this and can use d3d in all situations.
But this is achieved by forcing the polarity flags to zero. Although there's a separate setting to set polarity, it seems the other one has priority over this. This is most likely the issue you're seeing.
What are the downsides to the current config (CRT-Emu 2.0beta + vmm 1.4b) ?
Downsides are mainly on my end, when you spend a year on a project you expect it to work in all situations, rather than having people resorting to the old version to workaround unexpected issues.
Apart from that, obviously, you're missing all the nice features of the new VMMaker (which aren't still documented because we're just starting to use it).