1: Bea is a genetically engineered being that was created from scratch, making her a unique bug-like bioweapon.
and before that same organization that made her got into creating their own life, they experimented on Clara mutating her into the beast she now is, her original species is a mystery.

2: I don't think "smartness" is something that can be easily measured, and it also comes in many different forms.
Bea can be hyper competent in action and at picking up new mechanical skills, but still have large gaps in her knowledge due to her inexperience with the world and a lack of social connections.
meanwhile Clara might act reckless and crude, but is actually very street smart and good at reading situations and talking things into being in her favor.
at the end of the day, they're both cool and stupid in their own ways :>

3: they're both presumably Pan/Bi. although Clara is much more open about her sexuality than Bea.