But yes, you're right -- Bazel is the most correct monorepo solution. We started with a combination of the second structure, poetry, and shell scripts but have since moved to nix.
I use nix btw.
I think, in the long run, something like nix will win out. It makes sense for your OS "package build system" to be the same as your project build system.
If your python project depends on some mildly obscure python lib, do you write your own nix "package" (or whatever nix chooses to call them) wrappers for each release you end up using? Any other tripwires in your experience so far?
Specifically, we use this nix project [1] which provides a nice translation layer between a poetry project and a nix derivation. It allows our devs to use poetry where they want (with local relative paths in the pyproject.toml) and ci/cd to have more granular control of deps at build time.
There are some corner cases. As you correctly guessed, some more obscure python libraries might require a few extra lines (i.e. to specify that this package needs setuptools etc). of code.