Two questions:

Is there a weather mod that doesn't rain indoors, or is it impossible?

In Robco Certified i can't get my robot to be...useful.
If i set him on aquire hidden targets he keeps flying off into the distance, or up/down floors in a building getting himself killled, or me killed when he ignores closer targets.
If i set him on not aquire targets he just ignores everything, not even firing the 10mm pistol i gave him, with similar results as above.
What am i doing wrong?

In a true interior cell, like Moira's, you shouldn't have rain. If you mean you want it to collide with meshes so if it appears you are under some kind of cover outdoors, then there is no way to prevent this (has been an issue since Morrowind).

Can't help with the RobCo issues, I tried it only briefly and decided I didn't feel like using it.

I read somewhere a while ago that weather mods always make it rain indoors too and there was no way to fix it. Thats why i haven't tried one.

My only suggestion for this is to ditch Robco and go for "buildable bots". Its a more stable mod and I just prefer it. Robco never really worked for me though.

No, the rain will go through solid objects like roof plating and such (the rain has no collision data for it, so it just passes through), but the creators tend not to set weather patterns for interior cells. Granted, buildings built in the exterior will have the issue of rain falling through, but those are rare at best.

All in all, try a weather mod, they are absolutely worth it. I recommend Dynamic Weather by Xepha, myself.