I usually have space considerations with external return pumps, so installing the flange on the outside frees up space outside the sump. I do mine that way out of habit more than anything else.
Also, for RR type tanks with drilled bottoms, keeping the flange/gasket on the inside (wet side), the weight on the flanged area from pipes, ect, is pushing down on the gasket, keeping the seal intact. Putting the flanged/gasket on the outside on a tank bottom, has the pipe work pushing against the seal.