O’Reilly is an excellent publisher. My point, and the folks at O’Reilly will support this, is that a writer has to be their own advocate. If you are concerned about something, say so. Have a question? Ask it. They go out of their way to prep writers on the process, and that’s more effort than most publishers take. But the message is: you are the writer.
I’ve had a good experience writing books for O’Reilly, and most O’Reilly authors I know have few complaints: rare for the industry. Didn’t mean to imply otherwise. You’ll hear amazing horror stories from authors about their publishers, but I’ve heard almost none from authors published by O’Reilly.
My point in this post is that even when there’s a great relationship, the writer is still at a disadvantage: their book will always be more important to them than the publisher. And this isn’t the publishers fault, it’s the nature of the business (same for other creative businesses like music, flim, etc.). I can write maybe one book a year, while they, and especially my editor, are working on dozens: I will always have more at stake in a book that my publisher does.

Its entirely normal for copyediting to be restrictive: editors wait until the manuscript is very stable before doing it: why check from grammar in a paragraph that’s going to be entirely rewritten? So that’s normal. If by “loose ends” you mean fixing typos, cleaning up footnotes, that’s probably fine, but ask your editor: don’t assume what you think of as a loose end is the same as what they think it is.

O’Reilly, or any publisher, will naturally look out for your best interests at least as much as it overlaps with theirs. But more specifically: know your editor. They’re all different people and have different strengths, attitudes, opinions and experience. Even within one publishing house, two different editors can have wildly different approaches or talents. The better you know what to expect from your editor, the more you’ll know what to take care of on your own.

Let me know if you have more q’s: but mind you I’m still new at this. I’m only on book #2. There are plenty of folks, including O’Reilly authors, with way more credits to their name.

As we are coming down the home stretch of the writing and editing phases, I’ve so far not been involved in any of the copyediting of the book. I’ll have a chance to review the proofs, but I have been told that only minor corrections could made at that point. We’ve gone through many editing reviews already, but there are some loose ends that I’ve just been assuming will be cleaned up during copyediting. Was this the case in your situation? What should I look out for?

Otherwise, I’ve been assuming that O’Reilly is looking after *my* best interests in all other respects. Are you suggesting I shouldn’t necessarily assume this? Maybe I’m reading more between the lines than you intended.