For the most part, I think I've finally (functionally) solved the issue by disabling the DX9 half pixel correction on line 837 of UIPanel. Disabling that line has fixed almost all symptoms of the issue except for one or two (read below). It also confirms what I suspected, which is that pixel padding around all sprites in the atlas is actually not needed when using point filtering. I no longer have any texture bleeding or half pixel gaps, and I've been able to remove the 1 pixel padding around the sprites as well. The fix also makes sense too, since I was not seeing those symptoms on any platform except for Windows (and a tiny bit on OSX, read below for that).
It seems that the code that you're using on line 837 of UIPanel needs some revision. I don't think anyone's noticed this issue so far because: it's only a half pixel change that's usually hard to notice, it's mostly hidden by linear filtering, and it's only visible on Windows systems.
The only remaining symptoms are that random quads of a Sliced sprites are being distorted. I see this symptom on all platforms though so it's probably a totally separate bug. I've attached a screenshot of what it looks like with this post. There seem to be two workarounds...
1) Use a proper SD atlas for SD mode instead of an HD atlas with 0.5 pixel size. (right now I'm cheating and using an HD atlas for both modes)
2) Use different dimensions for the UISprite that make the UV math happy. (being even and a multiple of 4 is not enough, apparently)
As for your suggestions: I just need to figure out the problem with Sliced sprite, but everything should be pixel perfect already - I frequently do a sweep over my UI check for corrupt/bad values. All sprite dimensions are already divisible by 4 as well.