I’ve just noticed this. I suspect that the low pressure on the upper surface of the wing is a bit of a red herring.
The lift force is generated over the whole wing area to counteract the aircraft’s weight. Fuel fillers are not large in comparison. A back of the fag packet calculation for my aircraft shows a (very rough and over simplified) figure of about 0.1 kg. Lifting liquids by vacuum / lower air pressure is not easy at all unless you have effectively the straw in the drink itself as it’s always easier to extract air in preference to the liquid.
Given a rigid fuel tank I strongly suspect that the biggest factor in fuel loss is fuel sloshing and perturbations to the liquid caused by movements in the aircraft.
I would just assume the loss of fuel (actual or imagined) to be part of POH numbers 
If we do the maths it is the ratio of the hole surface to fuel surface should appear somewhere in the “hydraulic transmitted force”, regid tanks will do the rest…
