I thought that the Thargoids were allied with the human in the Lore? Well at one point anyway .
The Thargoids weren't "allied with humans". Some humans (in the Alliance) chose to try to prevent an attempted Thargoid genocide perpetrated by some other humans (in the INRA). The Thargoids were grateful to the humans that helped them but they are probably still wary of us as a species, if not outright hostile, given the whole "attempted genocide" thing.
On the issue of "Aliens other than Thargoids", it's what I've always said: check out the
list of permit-locked sectors over in the permits thread. Most of those sectors are bigger than the entire sphere of human space, and there's 17 of them. If they're all occupied by just Thargoids, then we're doomed - we can't hope to compete against an alien empire that's that much bigger than us. But if there's Thargoids plus 16 other races (or even just 6 other races), that makes for an interesting galaxy.
Universal Cartographics obviously has a mandate of some kind to slap a sector ban wherever there's even a slight whiff of alien activity. Either that, or Universal Cartographics has already been infiltrated...