Agreed that it’s not very user friendly, and frequently encouraging users to modify that config file would likely lead to more breakages/support requests. I was mainly thinking of developers that want to do fancy things with cumbersome-to-vendor packages, that may not bother sharing at all otherwise.
That’s a well-shaven yak you have there! 
One potential middle ground between users modifying pyproject.toml and add-on authors bundling the third party add-ons might be to do the vendoring after add-on install. The add-on could detect a first-run scenario, and use Anki’s bundled uv to install the platform-specific requested packages into a vendor folder inside the add-on.