would you be able to put a spacer on the inside of the tire?, that would shorten the lengh they stick out
I was thinking that myself. It would depend on how thick the bike tire is versus a snowmobile track. Based on how thin they feel (at least once most of the rubber has been worn off), I'm thinking they are thinner. If so, then you could probably add some washers between the head of the stud (push through type), and still have enough of the threaded stud sticker through the tire for the nut and backer plate. That way you may gain 1/8 - 3/16" clearance.
I don't think this would cause an issue with a tube, as you would probably still use an old tire carcass inside the tire to protect the tube from the studs. That plus the fact that snowmobile studs have a pretty smooth surface as the idler wheels need to roll over them in a track.