So then how do i "UV map in game"?
Smart Alec.
Knowing how to UV map correctly will result with aligned textures in game.
Just because it shows it one way in blender and another in-game doesn't necessarily make it the exporters fault.
Same thing for any 3D modeling suite.
I've used blender just barely, I'm not too much of a expert.
But, I suggest exporting a simple cube with a UV mapped texture and go from there.
Check all of your values, etc. Consistency is key.