You can do this with pre-built images. They can just install different packages on the rbpi3.img and the rbpi4.img, one with wayland one with x11. If you don't

You can do this with pre-built images. They can just install different packages on the rbpi3.img and the rbpi4.img, one with wayland one with x11. If you don't want to use pre-built images you can also do this with metapackages.