I remember having issues like that with under armor tops. They want to go to the thinnest part of my waist, no matter how long the top is, so they just bunch up and I get burned on my low back.

My sister has safety pinned her shirt to her shorts during a tri. I guess that's also a pain if you need to pee...but I wonder if maybe you could sew (do you sew?) a couple snaps or something to your top and your shorts that would make them stay together but not be so hard to undo. I don't think the new shirt would need much encouraging to stay down, but it needs to be stuck to something.