I don't agree with "stagnating", but yeah. I don't agree with just focusing on quads at all, so IMO his approach is good, of course, because I'd rather he did PCS first, too. But concerns are probably there for the future. I think the "decrease" in rate was fine honestly, because he did deliver great technical content and good PCS both at the same time this season (he was struggling at it the last season, except at Worlds). It was to be expected, and it was fine, for me (and really, nothing can compare to how much he improved between his first and second season, that was a transformation!). He's working towards it, and he had to split his focus! Now that he has a strong overall base, I bet we see a lot more development. (Though maybe you meant "progress overall", in which case, sure, he made about the same amount of progress, as he was able to land jumps much better this season.)
I doubt his team is clueless, but it's also true that very few coaches apart from Orser (and maybe really no one else at all, if you consider quality) have been able to get their skaters to do transitions into quads well.
As for jump "fluidity", he's still got more way to go. His flow-out now is not bad at all, and he gets it out of all quads now (I guess his bad habit of landing on flat edges has been worked through, and of course he's got softer knees and stronger ankles now), but he's still not really close to the flow-out Kolyada and Yuzuru get. Also, if you notice Yuzuru on his quad combos, his tagged-on toeloops look more like one fluid motion. Boyang does the technique there properly I'd say (he doesn't twist his body into it, like many do), but he does need more practice there, I think. (In the sQuad thread, someone called it "snap" I think) It's nitpicking of course.

It probably takes time to master it. (and he has it on his 3Lz-3T)
He's clearly working on his SS, and it does show in all parts of his skating, so "stagnating" is perhaps not right, and he definitely has improved in the areas you mentioned a lot, even from last season. He wouldn't have been able to pull off his SP this season, otherwise. He was really mature in his presentation there, and that's definitely a good development -- one of range. And he committed to it really well! I guess I still see a few of the same issues from last season to say he was improving on his
PCS at the same rate (especially in the LP, but that was also just a bad program). But that's not to say there was only a little improvement. There was a lot of it, especially in the musicality/IN area.
Also, to some people, his progress isn't enough for whatever reason (I don't agree with all parts of those criticisms, because they almost always begin with how he was "very bad" in his first senior year and he's better "in comparison", and I utterly disagree there -- I like
both programs, though his LP was certainly not the best). I think (and another person I've spoken to, as well. I wonder how he'd fair with a tango now that he's older and a better performer, his performance is what made that SP good) he's improved the most out of anyone in the current group over the past few years, but we did also agree that he could've been a bit further at this stage. Again, nitpicking, and he's on the right path as you said, so just a matter of pacing himself, which he's been doing correctly, IMO. I'm sure he and his team all know what is right for him.