That's not true at all. A lot of string players learn to play in orchestras or chamber style, which means they're only playing with other stringed instruments, and they absolutely are taught dynamic tuning by ear, which uses just intervals.
This is a weird way of looking at it. String players aren't sitting there consciously thinking of their tuning as they play - they're doing it by ear in real-time. The tuning they use will be the one that best harmonizes with the other notes being played at that moment.
> And it sounds off for music that doesn't largely sit in a single key signature anyway,
That's actually where the ability to adapt tuning dynamically is the most powerful - it allows you to be in tune relative to other pitches being played in that moment, not just in tune relative to some absolute benchmark that nobody is going to be able to hear anyway (because almost nobody has perfect absolute pitch).
Well, that's your problem. You're using a keyboard, which doesn't permit you to harmonize dynamically the way an unfretted string instrument does.
Even within a particular key, the pitch that sounds the best for a particular note will depend on which other notes within that key you're attempting to harmonize with. A keyboard can't do that.
"Unfretted string ensembles, which can adjust the tuning of all notes except for open strings, and vocal groups, who have no mechanical tuning limitations, sometimes use a tuning much closer to just intonation for acoustic reasons. Other instruments, such as some wind, keyboard, and fretted instruments, often only approximate equal temperament, where technical limitations prevent exact tunings.[4]"
It was routine even in my high school brass section to pitch down the major 3rds.
the most important element here is how it sounds to our ears. not how closely it tracks to an equation.
And you're right, we don't play "based entirely on just intervals." What we do is constantly adjust our intonation depending on whether we need it to be "just" with respect to something else (like other notes in a chord), or whether we are free to use a more "melodic" intonation. See https://www.youtube.com/watch?v=QaYOwIIvgHg for a good demonstration -- note that he talks in formal terms like "play x in the Pythagorean system," but I think you can largely see this as a rationalization of what players do naturally).
Finally, the presence of vibrato doesn't really obviate intonation concerns, sadly. There's a lot of theoretical debate about how the pitch of a vibrated note is perceived (is it the highest pitch in the range that determines whether the note sounds in tune? etc.), but in practice you can easily verify that adding vibrato to an out-of-tune scale will not make it sound any more in tune, nor will adding it to a shift mask a slightly-missed shift (if only!).