The gearcase halves were bolted together at the factory and line bored as an assembly. It is for that reason that they are indeed a matched set and it is not recommended to swap them. That said, their tolerances must have been held quite closely during the time they were making those 2-piece cases (which was a long time). I have bought several motors that had them swapped and have also swapped them myself, I had one that was difficult to seal up but still sealed. The others all sealed without issue and never exhibited any extra effort in turning the prop shaft due to bearing misalignment. I have swapped skegs from late 60s motors on to mid-50s midsections without any problem at all. I know it is not recommended, but I will take my chances on this one every time. I usually use Permatex Ultra Black geasket sealer on the gearcase halves. It works great for this application and is much more forgiving than the 3M 847 sealer for this purpose.
-Ben