You know it's technically impossible to ensure that the upgrade would work flawlessly with every possible user mod and devel application?

Yeah, the application manager UI could handle conflict situations better (at least give more informative error messages) but they still can be resolved without reflashing with some basic Linux knowledge.

If you mod/hack/install devel stuff you have three options:
1) Learn how the system works and become knowledgeable enough to solve your problems
2) Ignore the warnings, then reflash and/or whine on the forums when the system stops working
3) Stop messing with stuff you don't understand

I'd suggest either 1 or 3