yeah i haven't been able to find a fix either. then i've seen practically no topics in regards to borderless windowed being off-center since everyone apparently just gives up on it and uses windowed fullscreen. fullscreen is the only mode that runs well for me, and that's only assuming i don't task switch. the more i task switch, the worse it runs.
i'm not sure it's entirely tied to beefy gpus or fps being unlocked either--at least not solely. i'm running what's basically low end nowadays (r9 380, i5 4570, 8gb ddr3) with fps capped at 60 and still run into the same issue. exactly as mentioned in the op--fps is smooth at 60 and doesn't fluctuate according to overlay or logs but it just gets these tiny little irritating jitters that worsens over time.
i actually think i had the same problem in nier automata, except that game's fullscreen didn't poop the bed when i task switched so it wasn't quite as annoying. with destiny 2's reliance on third party apps due to a lack of in-game tools/qol it'd be nice if i could comfortably task switch.
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Switching to windowed full screen fixed it for me.