Installing dependencies for a pip-only package through conda

pip and conda are two separate package managers. Only in very rare cases package managers actually work together. In practical applications conda and pip usually do not.

In reality, mixing conda and pip packages is usually unavoidable. This often leads to a messy package management, as you describe.

In my opinion, the best and currently only proper way to solve this problem is to create a conda package for all (pypi-)packages and dependencies you want to use in your conda environments.

conda-forge is a community effort that offers an easy way to contribute your own package to the conda infrastructure. You may want to check out if your package is already available, and if not if contributing is an option for you.