I'm not really tracking the MHz signals thing considering there's the 10 MHz oscillator. It would've been interesting to see an EMI/C report. Usually I can see SMPS frequencies as a spur (especially in PFM mode).
For the 32K, at least for the H7 they recommended a ring of ground around it for some shielding. Unsure if that would've helped here. There are also micros that can use their internal RC 32K on vbat. And ones that can do USB without a crystal. The best micro is the one you know, the second best is the one you have. Maybe that's in play here.
The LED driver variability was nifty. My first reaction to large IO with tight timing would be an FPGA, but I don't know if they'd like the variable bank supply. It would probably be fine bit the solution used is interesting and works.