Ive never had to use bolts to pull the housings together. A light tap with a rubber mallet yes but once down i didnt need bolts to "hold it" down as such.
When you say diff seals, do you mean driveshaft seals? As they wont have any impact obv.
If the input shaft bearings aren't seated all the way to their correct location however you could be essentially forcing the entire shaft downwards when tightening up and this is binding against the other end of the housing.