There is always a possibility, in any experiment, that some unknown effect was the main cause for the obtained measurements. This can never be ruled out.
The reasonable way to approach this is to first ask what is our null hypothesis. In this case we would like to test general relativity, so our null hypothesis is that there is no relativity and that Newtonian mechanics -- the previous successful theory -- will be able to explain the experiment. The alternative hypothesis, which is the one we would like to test, is that general relativity is correct.
So now we have two predictions for the shift in the clocks. For this to be interesting the predictions should be very different, compared with the experimental sensitivity. We carry out the experiment, and if the result 'agrees' (in a statistical sense that I will not go into) with general relativity, then this is evidence in favor of general relativity. If the results 'agree' with Newton, this is evidence against general relativity. If the results 'disagree' with both, it is evidence against both theories.
Either way, the experiment does not prove that GR is correct or incorrect, for example because of a possible unknown effect. It can only increase or decrease our confidence in GR, namely it can change the probability that we humans assign to the statement 'GR is correct', and even that is only within the regime of parameters where we can carry out experiments. The best we can hope for in science is to have theories that we are very confident about.