I think the biggest peeve people have isn't so much that Fathom v2/PRO is closed source, but rather the "we'll open source it soon" kind of "dangling the carrot" stuff.

In the GitHub issue you mentioned "since people are confused [..]", but people are confused because your communication has quite frankly not been very good. Even today just looking at the Fathom README it's not at all clear that Fathom v2 (or "PRO") is an entirely different codebase/product which merely shares the name and branding, and not much else, and it's not clear that the "Lite" version is essentially unmaintained either.