It’s a moderate level of work with some manual testing if one relies on flatpak-builder being installed on the host system. AppBundler so far distributes all tooling via Yggdrasil, and putting flatpak-builder there is a hard problem — it appears that flatpak-builder and the Flatpak runtime are interleaved, which couples it to the Linux kernel and makes the tooling very difficult to bundle independently.
That said, it seems feasible to build a Flatpak package using OSTree alone, which reduces the question to whether OSTree can be cross-compiled with a Yggdrasil recipe. I don’t have an answer to that yet, but it’s the first thing to figure out.