Long story, but we started working on our toilet on Monday, and won't be able to finish the project until Saturday. Currently, our toilet is not connected to floor/wax ring/etc (disconnected) and it has no water in it or very little water in it. I can smell gas. Is this to be expected? The toilet is over the pipe, just in now way down as it should be and again, very, very little water in the toilet. Is this something I should be super concerned about? Sorry if this is a dumb question.

Sorry, I can't type/think today. I meant to say "just not way down" as it should be, however that doesn't make sense either. Okay so what I mean is we don't have the wax ring down, and it's not bolted to the floor.

Yes, you could very well get sewer gasses escaping from the sewer pipe. Remove toilet and stuff rags in pipe until you permanently reset the toilet.

The Widget Maker nailed it, You now have a open connection between your house and the city sewer allowing sewer gas to escape.
Sewer gas is a health hazard to your families health and the methane content makes it explosive, Follow his advice and seal the hole, Good luck, Tom