Theme API could be an improvement, but it isn't a perfect solution either - because the same complaints with the same arguments show up in relation to distros patching application code. It's a general problem of who changes the software. Some FLOSS developers seem to desire to have "producer/consumer" relationship with users of their software, seemingly forgetting that
the entire point of FLOSS is to make this relationship model impossible to enforce.
I don't see a good technical solution here, but I see two social ones: a) developers of FLOSS must understand they're writing software that can and will be modified and re-released by others, sometimes individuals and sometimes organized groups (like people making Linux distributions); and b) users need to understand that if they have a problem with their software, they should reach out to people from whom they got that software for support. If you got a program from developer's home page, you should contact them directly. If you got it from your distro, then distro maintainers should be your first line of support.
(Also c), some users won't understand b), and forwarding support requests to appropriate people is just part of publishing FLOSS.)