Big monolithic Python projects will face dependency issues for sure. However, softwares structured into simpler, smaller components, using the right languages for the right tasks, will probably have simpler dependencies for each modules.

That's what Go and tools like Bazel allows for : static builds, which forces to modularize the project into smaller independent components.

In case of static builds, the protocol between components is the C ABI, or an RPC protocol, but it could be a mesh of microservices too.

What is currently happening with the explosions of tools with Python is the result (take it with a grain of salt, only my opinion) of people only working with Python and not exploring enough outside of it