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I don't think there's any in-depth documentation on how scaling works per se, but just from PQ code it simply scales the character's transform by the value calculated from the position in the current region, and then the pixel-perfect camera effectively applies the "nearest neighbour" interpolation to the result. So the unpredictable result at lower scales is sorta expected.

Don't think there are built-in solutions for your case. And in case of overlapping scale regions, it looks like instead of combining the scales, it uses the values from one of them, which is not really useful.

I'd recommend joining the Discord server and asking in the general chat or creating a topic, the discussion over there is much more active

Is this for pixel art? Generally this is solved for pixel art games simply by designing them so that you dont have to scale characters. It's something I learned early making games with AGS, that scaling pixel art never looks great. So now I always avoid scaling up, prefering to shrink down the room instead as a cut-away.  And I tend to do room art with the character in them so I can avoid too much scaling down too.

For hi-res games, you also have scale control on the sprite importer, so that might be what you're looking for.

For the other scaling issues, it's hard to know what you mean without screenshots/vid maybe?