Does anyone know how to get the game to run in a window instead of full screen on the Mac version?

It's the same for all AGS games - you either use winsetup.exe in the game folder or edit acsetup.cfg (which should be in the game folder too).

This is what I was expecting, however neither of these exist in the game folder. This game appears to be packaged differently than other releases of AGS games.

Hmm, maybe they are somewhere else. Try searching for them.

What I ended up doing was copying an acsetup.cfg file from Resonance into "A Golden Wake.app/Contents/Resources/game/A_Golden_Wake.app/Contents/Resources", removing everything except the windowed=1 setting and it works ok. The final acsetup file looks like:

[misc]
windowed=1

This opens the game in a window.

Unfortunately the other issue is that unlike other games (like Resonance) the game does not freeze when hidden.

Nice solution. You can also copy winsetup.exe from Resonance, but you would need to rename the main .exe file to Resonace.exe (or whatever is the proper name for this in Resonance folder) to make it work.