The problem with two 3A isn't actually his lack of 3A-3T combo. I'm pretty sure that Nathan could do it if it was necessary, but it's the fact that he can only repeat two jumps, of which only one can be a quad, and currently he is already repeating the 4T and 3T. To repeat the 3A, he would have to remove one 3T, and in order to maximize his combos, he would have to add a 3Lo combo, or what I have been secretly hoping, a back-half 4T combo, which he has been rumored to do in practice sessions.In terms of long term strategy, there’s no point in trying a five-quad and double 3A layout unless he gets a 3A+3T combo. He loses more point from downgrading one of the combos from -3T to -2T than he gains from upgrading the 3Lz to the 3A.
Now, I don't really think it likely that he will do a back-half 4T next season, as it wouldn't be enough time for him to really stabilize it in competition for the Olympics. His technical score is so much higher than everyone else, there really isn't a huge incentive, especially as a quad-quad combo is not currently allowed in the SP. As for the 3Lo, he has never done one in competition, though I have seen video of an eked out one that wasn't particularly pretty.
I know Rafa in a lot of his interviews seems really gung-ho about increasing the difficulty, and that the clean 5 Quad programs aren't that special in comparison with his much harder layout in 2018, but this year he has successfully raised his SP base value to be as high as it can be without a 4A. If Nathan chose to switch his 4F in the FP at WTT again with a 4Lo, I would find the 6 quad program to be more likely for next year.