One thing you can do (I'm not saying it's user friendly) is set up the tool in a virtualenv and then set up an alias like
alias foo-tool=/home/blah blah/tools/something/env/bin/python -m foo-toolCan you give a concrete example of an installation you attempted that failed?
The package versions are however fraught - our machine learning codebase at work only was stuck on the 1.x versions of numpy for more than a year, as scipy and ultralytics both took forever to upgrade, and that prevented us adopting packages that depend on the 2.x numpy.
But the language isn't designed to support multiple versions of the same library in the same runtime environment. If you get them both to load (and there are a lot of ways), they are different libraries (actual different module objects) with different names (or the same name in different namespaces). Packaging tools can't do anything meaningful about this. I write about this on HN more often than I'd like; see e.g. https://news.ycombinator.com/item?id=45467514 . It's also covered in https://zahlman.github.io/posts/2024/12/24/python-packaging-... .