I enjoyed this one -- the answer adjustments made those clues just a little more tricky to track down in a way I found nicely challenging but not overwhelming. It took me a while though. And there are some clever clues here.
I have one question, which I'd appreciate a nudge for just to set my mind at rest. I don't see the wordplay for 1a. I know the adjustment, and the definition, and just don't see where the Roman art comes in.
I do see what people mean about the rubric, although I have to say that what was intended was immediately clear to me: I think it is reasonable to expect endgame changes to have some relationship to what has gone before even if the rubric doesn't call that out explicitly, and I interpreted "making new words or phrases" to mean that ALL affected entries would be new words or phrases. However, that last point could perhaps have been clearer: "leaving only valid words or phrases" would have perhaps been a little more precise. It's not quite right to describe the final two rows adjustments as "thematic", I think -- the theme is the treatise and its subjects, and the adjustments at all stages don't have a direct link to that theme. Perhaps that sentence of the rubric should have said "solvers must *similarly* adjust the entries...". But I have to say that I found any unspecificness of this rubric FAR less than we had for "this page is intentionally...", though...! Many thanks Poat for an enjoyable puzzle with only minor criticisms all round this time :-)