> the project owner can choose which build backend their project gets built with

When following an automated workflow implemented by an installer or other tooling, yes.

But you own the sdist file, and the archive contents, after downloading it. Nothing prevents you from editing pyproject.toml, using a build frontend/system that offers a flag to disregard PEP 517, running your own custom scripts on the data, manually copying the files into the target environment, or whatever else you can think of.

And since Gentoo is doing its own packaging with its own package format, nothing prevents them from doing the same kind of patching.