You are right on the same path that I am. The possible exception is that when I play scales on the bass, it is usually against a drone, or I am imagining a tonic drone, so I am shooting for just/pure intervals because they make more sense in that context. As for the rest, I agree with you.
I made a recording with a string quartet and piano last year. The players were top shelf pro players, and all followed their instincts. Before the piano entered, the intonation was just/pure. Once it entered, I was instantly with the piano, and the quartet took a minute to come around. “Pure” means in tune with what is actually happening now in the moment. If the piano is playing a tempered major third in a chord, you go with that, because it can’t adjust. If you play just 3rds against that, it sounds bad. If that means you are now playing it technically sharp against the root of the chord, that’s how it goes. You serve the music that’s actually happening. Full Stop. Be “right” and sound bad, or accept reality and sound less bad. Is that actually a real question?
I guess that’s why I prefer the term “pure” in the final analysis. One of the forum’s longest term members, a person I very much respect, has the user title “inadvertent microtonalist”, which is meant to be a form of self deprecating humor. But really, it’s a form of honestly that is all too rare these days. We are constantly adjusting. We adjust to what’s actually happening. That’s what musical life, and all life, really, actually is.
One of the points it has taken me years to formulate as a concept, which I hope to highlight in the third installment, is that when you are playing with an equal tempered instrument, what you are actually doing is playing in just/pure intonation with the unison or octave that the equal tempered instrument is actually playing technically “out of tune” by x cents. So, instead of playing technically out of tune in theory, you are actually playing technically in tune in practice. The challenge is going to be making that point in a logical and intuitive way that resonates just like the practice of intonating that way does in any given moment.