You're assuming your concerns were dismissed arbitrarily. Why? Is it possible that your concerns were considered, pros and cons were weighed, and the final decision was simply not in your favor?
And what's this nonsense about "my computer, not the app maker's"? How do you think project governance works? Decisions are made, and every single time a subset of users are disappointed. That subset isn't having control of their computers taken from them. This stuff is happening out in the open, for free, and with express permission to override any behavior you want with your own patches. You can even distribute your patched version, also free of charge. It's downright humbling how free we are when it comes to bash and OpenSSH, and you have the gall to come out with "My computer is mind, not the app maker's"? Do you have any idea how low the bar is for user respect in the average app? How much money can be made if you're willing to disrespect your users? And the bash and OpenSSH folks would never, not ever consider any such breach. They have stayed firm, despite world-blanketing success, in their user-respecting free software ways.
And for a disagreement of where to put config files, you'd lump them in with the user-hating rabble that makes up the rest of the software industry. We're surrounded by people who actually do arbitrarily dismiss user concerns (because the users are the product). People who actually do believe your computer belongs to them when you use their software. Please, in the middle of all this shit, keep in mind who your best allies are and just have a civil engineering disagreement with them, without insulting them.