To speculate the B61 is a dumb bomb. And most photo's of the casing show no plug/contact point for electronics. I'm assuming at take off. When the neutron reflector's distance is set, and the barometric pressure for denotation height is calibrated.
Yeah, my guess is the bomb is armed and the yield and other parameters set just before the aircraft is set to taxi out for takeoff. Some part of it must be done on the ground, because no US nuclear weapon can be armed by a single person.
It wouldn't have to have a port. The US has had radio programmed artillery shells for a long time so using the same tech to set and arm bombs isn't a stretch.
These are just proximity fuses. I can find no reference to actual communication with in-flight artillery shells. Furthermore Nuclear Artillery shells were armed when loaded. They were one of the few systems outside of the two-man rule. As a single inferior officer would arm the shell when loading it.
I wonder if arming of a bomb like that has a time limit - so that it safes itself if not "used" or explicitly deactivated within a particular time period.