It would absolutely make a difference. You would go from excellent to maybe spotty with drop outs during turns. It has a circular polarized antenna which needs to point to the sky. Try putting it inside the fuse. If it's just covered by thin plastic like a canopy it should work fine and be protected.
I put it in the fuse near the tail with the antenna sticking out the top. I have a video transmitter and data antenna in the near vicinity, do you think they will cause problems?
Not much difference with the interference issue between on the ground and in the air. Fire it all up and see if you get a lock. You can also insert a debugging statement into whatever code you are using to print out whenever a checksum error occurs in the gps parser. Lots of checksum errors is a good sign of too much interference.