WOW, that was it, suhosin was the culprit. I recompiled Apache with the same exact settings as last time except I removed suhosin.
Everything just works now (just like the Processwire I know and love)
Image uploads now work even while using the deprecated CropImage module on an 2.7 install (upgraded from 2.3), inside a repeater, which was previously simply unthinkable. (not using this in production, just doing an upgrade on an old site and thought to check).
The server is even a lot more responsive, the time to first byte decreased from 2-3 seconds to 0.6 seconds, and that was another problem I was trying to solve.
Suhosin is now officially a plague upon humanity as far as I am concerned, I can't believe I didn't know about its effects.
Thanks so, so, much Ryan and everyone else who helped! So happy I could dance right now
Now, about that payment?
I normally run much tighter permissions, that website is not a live one, I just used it to try and debug the issue. It had those permissions left over form when I had a different PHP handler that required them and I left them like that to try an rule out any permissions issues. The suhosin issue was happening even on 640 permissions.