I've done a bit more testing, with a fresh SD image. I used raspi-config to set the system to Wayland or X, rebooting each time. What I see is the opposite of what you saw - a vanilla Miletus 64-bit app is OK with X but has a corrupted display with Wayland. This was all with VNC disabled.
Then, with X running, I enabled and connected over VNC and it was still OK.
Dave