I am pretty sure that is how they are supposed to be. The newer versions of stainless steel rings are bigger, give you more play. As long as the carbon ring fits into the bellows well, and the ID of the stainless steel ring is the same as the old one you are good. Remember the carbon ring is supposed to float on the shaft an not touch it. Only the stainless ring need to have proper clearance for orings on the shaft.
Since you have gone through the trouble to take this all apart I would also replace the bellows as well, they tend to loose their rubber 'spring' over time and you may not have a good seal. May also wish to replace the 2 orings inside the PTO oil seal, would suck to have an oil leak after you put it all back together.