Yes, ernie-f I'd say you are right on target.
You are not just complaining, but are talking about very real issues for those of us interested in publishing books. Sadly, AF Publisher does not meet a professional standard.
I started with Quark and moved to InDesign many years ago. I've been thrilled with owning both AF Designer and AF Photo and had high expectations for AF Publisher. I downloaded a beta version of it last year and saw it was not ready. But I bought a copy of AF Publisher a few weeks ago since I thought it would be ready for publishing primetime by now. Sadly, it's not a professional tool like Designer and Photo. Publisher is best suited for an office secretary doing flyers and, IMO, is not equal in functionality as AF Design and Photo.
I don't think the fact that that Publisher is cheap should be any excuse for it having key weaknesses, as you describe. After all, AF Designer and Photo are cheap but they are world-class professional tools.
My advice is that Affinity management tries to produce a 250-350 page book using it. One with a TOC, illustrations, footnotes, and bibliography. They would not be able to do it with any efficiency. Also, it's silly to just patch on the export module from Designer and Photo. Book creators need mobi and epub in addition to PDF, not all those legacy formats from their image software. Most are irrelevant since digital print publishing is mostly PDF-oriented these days.
I'm old enough to remember the term "kluge" as applied to computing. If something in programming didn't work, rather than redo it correctly, you would "hang a bag on it" making a technological griffin, which was a kluge. Sadly, I'm afraid that's what we have in AF Publisher at this point.