it's not like there are fumes anywhere but in the fuel tank.
jet-A itself is not that flammable at all. Don't know what all the fuss is about.
also it will not produce significant gases until at high altitude the pressure drops.
for a comparison with regular gasoline check this nice video:
https://youtu.be/7nL10C7FSbE?t=128
So any reason for leaving the fuel pumps off is more likely an overpressure / overflow / spill problem than anything else.
Matmax: i don't know what exactly why you point to TWA800 the fuel quantity indication system created sparks in the gases above the kerosene. that's obviously bad.
i'm not certain a fuel pump creating sparks would do anything while submerged in kerosene. the kerosene simply wouldn't care.
also what makes the time of refueling so much more dangerous than any other time?
the vapors should be vented in a controlled manner somewhere they dissipate.