Stuff+ is mostly each pitch in a vacuum. It does use the main fastball as the basis of the model and measures everybody's other stuff off of that pitch. There are other metrics that try to measure how a pitcher's entire arsenal interacts, each pitch with the others, but they are newer.
It would fail to take into account a lot of things. I don't think it captures "tunneling" at all for example, so someone like Pop could have a good sinker and a nasty slider but if that slider is recognizable immediately out of the hand, hitters just won't even try to hit it and/or they can destroy any mistake sliders. Something like that probably explains Zach Pop entirely, since his career run values are positive on the sinker but negative on the 112 Stuff+ slider.
Also important to note that not every pitch has a 100 as the average Stuff+. The typical Slider is a 110 pitch, so Pop's is closer to average. And his 105 sinker is actually a full standard deviation above the typical sinker, which carries a 92.5 mark. So he's more of a one pitch dude, with a boring slider, and not really a guy with two plus pitches at all.
Stuff+ is pretty good at telling how good a player is in small sample sizes. Again, similar to velocity. Just think of it like a better, scientific version of scouting grades.
It can be pretty dang useful in small samples but becomes less useful over time unless you are thinking about changes a certain pitcher is going through.