I'm going against the grain here, probably because I have a really sensitive sense of smell, but the garage area of our hauler smells after the RZR has been in it. It doesn't linger after the RZR is out, but it does smell. It's not really gas really, but just... equipment smell. I also don't like staring at the RZR when I'm in the living area of the hauler. Also, it's easier to contain a mess in the separate garage... whether that's from the toys, or our dogs, or us. So, being a wife myself, I'm with OP's wife.
That being said, as others have mentioned, every manufacturer has haulers with and without separate garages. Maybe a good option would be to narrow down manufacturers and then go from there. I also agree that to get a separate garage you'll have to go longer than if you are cool with an open garage. Our previous TT was about 32' and had a 10' garage (It was a Keystone Raptor 27FS, now sold as a Carbon 27). Our current 5er is 38' with a 12'6" separate garage.