So -- "whachoo say about that"?
I say you called it right by labeling your objections "nitpicking", at least regarding the windows.
I'll grant you greater discretion regarding the lines on the rim of the saucer, as they are a more significant change, but at least for me, I'll give Dochterman and the New Voyages folks the benefit of the doubt. It's their nickel. They can make whatever changes they want, especially because I know that James Cawley is an extreme purist. He doesn't make changes in a haphazard manner.
Any comparisons to the half finished Phase II model are questionable at the best. Who knows exactly what the finished product would have looked like? Beyond completing the basic build-out, there almost certainly would have been revisions. Look at the changes in the 11' model between the time it was delivered during the shooting of "The Cage" and the start of the series. The changes were small but, in the end, significant.
Plus any contemporaneous engineering drawings I've seen of the Phase II ship were more sketches than plans, including those of Matt Jefferies. The ones upthread here are the most complete I've ever seen, but I don't know their lineage. When were these "blueprints" drawn? Maybe I should read the book.

They show no details on the rim - windows, ridges or whatever. I'm sure it was never the intention to leave the edge clean. Most likely those details were to be determined at a later date.
Design is often an evolutionary process. I've recently found that out the expensive way, as I am remodeling my house right now. My latest change of heart will cost me $350. Sometimes you don't know what's right until you've done it wrong.