I've found that no amp setting allows me to hear myself in the way I'd like. That includes accurately hearing intonation. If it is loud I just throw my hands up and not worry. I've got a big amp but even in those situations I don't think the amp really helps with intonation, I'll sometimes put my ear up to the side of the neck to see if I'm at least close.
I've gotten to the point where I've been leaving my amp at home with greater frequency and just running a mic (an SM58 through the afterlengths) through the house system if there is one. I've put quite a bit of work getting a big sound out of my bass. If I can't hear my bass acoustically then all bets are off. For jazz especially amps just seem to cause more problems then they solve. If I am using an amp I try to make it just support my acoustic sound.
So bottom line. Especially in a trio setting.
Turn down.
Get bigger acoustic sound.
Get the guys you are playing with to be more sensitive.
IMO, IME, YMMV, ROTFLOL