Ok, I think even the drawing connections to Star Trek thing is too far between this and the toilet/pee corner thing.
On why, Isaac didn't use his weapons in the past, they may have been deactivated per his programing while on his mission for the Kaylon. He couldn't use them or didn't "know" he had them.
Agree on the Trek invisible correlations and the Isaac with the guns inside his head.
I think they were only activated after he went back to his home world.