If you want to keep a factory fan vent, I'm not sure.
If you are open to a passive vent (just an opening with/without a screen - and you could put a fan on the inside), you could go with a marine hatch. They are similarly sized to vents, and sit very close to flush.
I'm not as familiar with the automotive industry, but I think car sunroofs sit pretty flush. Not sure if they are curved for the roof or not.
Vintage Trailer Supply has two vents with a flat aluminum top. Same type and size as the standard 14" x 14", but flat topped. There is one that is a Fantastic Vent (has fan) and one "plain" one. Neither will be completely flush though. It's just that the lid is flat instead of domed. But I'm not sure if you just need "more flush," or if you need "100% flush." These might work if you just need a bit less of a hump.
Can we see some photos of your new baby?
PS: Some folks have made small-diameter plywood "wheels" in order to get their eggs into lower garages. Of course you need to have a relatively smooth surface to roll on. But that would give you quite a bit more clearance, and I would rather remove a couple of wheels than a roof vent!