I did some research and found distutilscross which seems to make setup.py aware of cross-compilation if a few environment variables point it to the desired configuration. So far so good.
Unfortunately installing python3-dev for a target architecture, eg. python3-dev:armhf, conflicts with native packages. I’ve seen this happen with glib2.0-dev before, but in this case it’s worse because it affects non-development packages as well and in the attempt I removed snapd among other important things. This seems like a no-go because it’s unusable on a desktop machine.
I’m going to look into downloading Python binaries separately to avoid this problem.