Ultimately, this. You can test for very, very small numbers, but you can't test for zero. This is why, for example, even though lead has no biological function, extremely small "acceptable levels" are specified in regulations rather than simply saying zero lead. You can prove that, for example, lead levels in the air are less than 0.15 µg/m^3, or that they are not. You cannot do that for zero (nonzero is easy to verify, but zero is not).
There is also, of course, the fact that no food is safe in all scenarios. Even pure water is toxic at high enough doses. For that reason, it makes no sense to hold GMO food to even higher standards than non-GMO food: equal standards certainly make sense, but not higher.