[ainarssems]

does it happen because they simply forget to connect something or because system should be 'airtight' for Bernoulli's effect to work and people just not assembling the damn thing with enough attention to airtightness?

Generally it's because of limited space, because you do not see anything and because of lack of knowledge and experience from the fitters. You either do it by the feel or you need to feed endoscope through the left side fuel level meter opening to see what you are doing. It's very easy to put it in wrong angle so that return pipe miss right opening in fuel delivery unit. If the o-rings are damaged it could also result in similar issues but in all cases I have seen it just has not been fitted properly.

Also, does the '2/3 tank problem' always appear as a side effect of incompetent repair? Can this problem appear on a car with no work done in the tank since new?

I would say very unlikely and I have not seen any with a problem develop on it's own. It's always been after some work was done in tank.