This is because CFF is mainly built to support the software citation principles [1], where it is argued (rightly so, if you ask me) that software is important enough to be cited in its own right.

Also, there will likely be no new paper for each version of software, so if you want to cite the version you have used in your work (e.g. towards reproducibility), the paper may be useless.

[1]: https://doi.org/10.7717/peerj-cs.86