When citing collective written works (like conference paper collections), the editors’ names are usually listed. I don’t see why not do the same here: cite the maintainers’ names when citing the whole, and also specific authors when citing particular fragments.

Why not simply cite the original creators? Then if major features changed amongst versions then the key contributors?

Original creators (whose idea the software is) should be first author.

As I understand it, an important point of software citations is to help academic researchers who are (unfortunately) measured by citation metrics. Will whatever tools the bean counters are using connect "the <project> contributors" citations properly to people? I don't see how they could.