It's important to realize that about:config flags aren't part of the official configuration interface, so there really aren't any guarantees about how the system will behave if you frob one. Generally, updates are designed so they don't interfere with things that are set from the official config interface (this is hard enough!) but a lot less care is taken with any other about:config settings.
Update: I think a much better complaint is that there's no official way to disable these features.