I agree with Pappy 'n Jasper. There's no need to worry about sealing the gap.
The only problem I can foresee is if the lower unit didn't seat right. There are at least three things to look at. 1 Water tube seating. 2 Shift linkage position. 3 Driveshaft over-lubrication; grease on top of splines preventing driveshaft from seating into crank. 4 Anything else in the way.
In any case tightening the bolts down always messes up something.
If the gap is from a damaged or imperfect surface, no sweat. If something prevented the lower from fully seating, then it has to come apart and find out why. It could have damage from being forced into place. Running it like that can only make matters worse....if that's the case.