BTW I was just looking at the Mistercade docs and it explicitly calls out supporting 640x480. I assume Expander will do it too, so maybe it just a software side problem to be solved at some point.I don't see why it should matter if you have it connected to the jamma edge connector. It's just a connector. But again, I'm not a MiSTer or an Expander owner, so I don't know.
In the meantime it seems like JVS-PAC or the like it probably an easier approach.