i would weld it up. sucks you have to take it all apart again. this only happen on cases that have inserts? looks like it makes the cases weaker there. also where did you support the case when you pressed the bearings in? have to support the case near the bearing not just have it sit on the case mating surface.
i don't think it would matter, if you pressed it in or used a socket and hammer. if the bearing goes in square, it will go right in and easy. cocked will take more force and something could break, crack. i always press in main bearings. never broke a case. used to use a hammer and socket, didn't like banging on the cases, so i got a little press.