If your project has any third-party dependencies, and so (nowadays) you're going to set up requirements.txt and virtualenv and whatever anyway, I can see that you're going to think things like "this XML parser in the standard library is just getting in the way; I can get a better one from PyPi".
But I think a lot of the value of a large standard library is that it makes it possible to write more programs without needing that first third-party dependency.
This is particularly good if you're using Python as a piece of glue inside something that isn't principally a Python project. It's easy to imagine a Python script doing a little bit of code generation in the build system of some larger project that wants to parse an XML file.
I think the biggest problem is going from zero third-party dependencies to one and more. Adding that very first one is a huge pain since there are many ways of doing it with many different trade offs. It is also time consuming and tedious. The various tools like you mention are best at adding even more dependencies, but are hurdles for the very first one.
Not true. The more external dependencies you add, the more likely it is that one of them will break. I try to have as few external dependencies as possible, and to pick dependencies that are robust and reliably maintained. There is so much Python code on GitHub that is just broken out of the box. When people try your software and it fails to install because your nth dependency is broken or won't build on their system, you're lucky if they open an issue. Most potential users will just end up looking for an alternative and not even report the problem.
[1] https://github.com/jazzband/pip-tools [2] https://docs.pipenv.org/en/latest/ [3] https://tox.readthedocs.io/en/latest/