it came across as valid issues with a tinge of whine.

Maybe it's because I'm not a native speaker, but I always understood "whine" as to mean: "complaining in an annoying way about something unimportant". So I'm replying on that basis.

I get that the "replication compliants" touch on a fundamental design choice in the way how the federation is typically working through ActivityPub. But that doesn't make their problem "unimportant". The conclusion I'd take from that is that either there's a need (for them, though perhaps for others too) to redesign Lemmy so it can fit that purpose or they made a wrong choice by using lemmy to build their platform.
I think at the moment they are debating which one it is.

As for whether the way in which they complain is annoying... well, given that it's a written text that can't transmit non-verbal cues, I'd suggest not making too many assumptions or reading too much into it. Any complaint would sound annoying if you make the assumption that it comes from a position of entitlement, try to second guess or recontextualize it in a way that makes it no favors.