Just to close the loop on this - USB 3.0 is working correctly for me after changing the PYNQ 3.1.1 device tree from this PR:
I also came across this post from a while back that has a link to the modified 3.0.1 image that Real Digital ships with their boards, which should also have working USB 3.0:
I’m not sure if there’s also a hardware issue on earlier revisions, or if the error described above was only in the old schematics, but fixed before the board layout was completed… but worth looking into if the above fixes don’t work for you.