From the Qt blog:
On the desktop, we have been working on Windows and Linux support for ARM architecture. The Qt 6.6 distribution does not include binary packages for those platforms, but you can make your own build of Qt 6.6 for those platforms using the same process as for x86 architecture. With Qt 6.7 we plan to make official ARM packages available for all desktop operating systems.
Since Qt 6.7 will likely see an April release I may just wait until then to deal with the Windows arm64 version. If the Qt6 build of Avogadro is at some point up and running as Win x64, macOS universal, and Linux x64 builds, I feel like arm64 shouldn’t be an issue.
Do you currently build for Windows by cross-compiling? That would allow me to cross-compile from my Linux machine and test my builds with Windows’ x64-on-arm64 emulation, which currently doesn’t work. I’m not having a lot of fun trying to set up Windows as a dev environment 
If I do further work on Qt6, where would be a sensible thread to discuss it?