I'm referring to OP's list of things they change:
> I want the browser to act as my agent, following my preferences in all things. I set a minimum font size, I control which fonts pages may use, I control when they may run scripts, when they may have videos or sound, what form controls (buttons, text inputs, etc) look like, when they may load content from third–party domains, etc, etc.
Some of these are privacy considerations, but most of them are also accessibility-related for some people. Ensuring fonts are in readable ranges for a given person, preventing autoplay, changing form controls to stand out more—all of these are things that people do to accommodate for disabilities.
This one thing that bugs you (rounded corners) is an aesthetic change, but the fact remains that you should expect browsers to modify your designs to meet user needs. If this serves as a wakeup call to designers that they can't count on pixel-perfect designs, good.