> # Add enough .. to point to the top-level project directory.
This suggests that there is more than one entry point to the Python project?
While I'm sure there are good reasons for this, and while I'm not criticising your instance of this specifically, as a general point of advice I've found this sort of thing to be a bit of an anti-pattern.
Having one entry that handles things like path setup and other global concerns, before delegating out to subcommands or whatever construct works best makes it much easier to keep the whole codebase aligned in many ways.
Django has a system for this and while it has its flaws, it is nice to have it. Using this, on our main Python codebase of ~400k lines, we have a single manual entry point, plus one server entry point. Coordinating things like configuration, importing, and the application startup process, are therefore essentially non-issues for us for almost all development, even though we have a hundred different operations that a dev can run, each of which could have been a separate tool like this.