Don't mangle `dependency-groups` syntax

[mrossinek]

I've been using dependency groups for organizing non-runtime dependencies of my package without bloating the optional dependency specifier. However, it looks like using extremal-python-dependencies to pin versions in these groups, mangles there contents to the point of actually loosing information (see e.g. https://github.com/Qiskit/qiskit-fermions/actions/runs/24559361757/job/71803848368?pr=69). We should check why that is happening and fix it.

[garrison]

It is great to learn about Python's support dependency groups -- I've been wanting a feature like that for a while now, and this is my first time learning about it. That said, I am very surprised that the relevant function seems to be losing information. I expect it to be modifying dependencies, optional-dependencies, and build-system, while leaving everything else untouched. So, it would be nice to better understand what is going on here. And of course, even better would be to correctly process the dependency-groups, too.