Hi, and thanks for supporting CFF through the Zotero connector (for GitHub repos) now :).
FYI, we're in the process of improving the website atm, including a Rationale section, etc. which will hopefully make it clearer why we think the format is a good idea, at least for the time being.
As for your takeaway 2.:
`references` can take all kinds of references, not just software and references, including articles, so a paper describing the algorithm implemented in the software that the CFF file describes is exactly in scope for that (the paper being, e.g., a prior work).