Entrances to the OSSS Base?

Because base that is fighting the aliens =/= the aliens themself? The alien ships are in every part of the maple world, not sure why you're connecting the entrances to the base fighting the aliens to the aliens themself.

Because the whole point of the Aliens is to do the quest, and you can't do the quests without entering the base. But storyline wise, you're right. Having aliens everywhere doesn't mean that the bases have to be everywhere, but its more of an annoyance to those who want to train, while also doing the quests everyday.