I only don't like the .venv in the project directory. It tends to get copied into git or docker. And it makes backup of a project a lot bigger and taking longer because of the many files.
Uv doesn't require .venv in the project directory, it's just the default. If you have a good reason why it doesn't work for your setup, you can place the venv dir anywhere and still use uv.
You shouldn't be making a backup of what's already in a remote git repo.
I don't know what's gone wrong with your Git setup (and I don't use Docker), but dotfiles (thus, a `.venv` folder) should be getting gitignored by default. (If all else fails, you can just add a `.gitignore` with just `*` to the venv.)