There are all sorts of things that are different about these guns that matter not one whit in GURPS terms. Mostly because pi = 3 in GURPS.
In character terms, they do the same damage and have the same range. They both can accept a lanyard. They have the same Acc number, but the Glock gets the bonus for Improved-Visiblity Sights (High-Tech, p. 156).
The Glock is lighter at 2 lb. and carries four more shots. Spare magazines tare at 0.6 lb.
While the FN is heavier (2.4 lb.) the 0.5 lb. spare magazines can pay off quickly depending on how many your character lugs around.
The "typical" gun and two spare mags comes to 3.2 lb. for the Glock and 3.4 lb. for the FN. The Glock is packing 12 more shots at the end of that so we'd have to be 3.9 lb. to get near parity with the FN. Any world where you can own the Glock, you can get the MecGar 15 rounders for the FN, which don't even weigh any more than the 13 rounders once the rounding is done.
A two big things that the game allows for on the Glock the FN doesn't have is being hammerless (Pulp Guns, Vol. 1, p. 8) and Very Reliable (B407).
GURPS does not generally mention things like safeties, but in my worlds I account for the magazine disconnect; the FN has one and the Glock doesn't.