I'm still not sure, but here's been my experience.......
For the first few turns, just keep away from the aliens if you want to be friendly.
After a few turns, ok to be among land-based aliens but don't attack.
If you end up next to a nest, move away the first chance you get. If I remember correctly, for Explorers, there is a virtue (?) that make it so aliens will ignore your explorers. Good to get for those expedition spots right next to nests!
It's my understanding that there are two different kinds of aliens - normal and Colossus. I believe Siege Worms and Krackens are in the Colossus category, so attacking them won't matter to the 'normal' land based aliens if you want to stay friendly. (Plus you want to get the Seige Worm quest complete).
Still not sure where Sea Dragons fit in. I thought they were 'normal' aliens, but I'm currently in a game where the land-based ones leave me alone, but the Sea Dragons are killing anything they find of mine on the seas.
Maybe they are on two different counters?