Yes, it may be the key.
If a pilot knows his fuel uplift, the aircraft's average burn time and has an understanding of the aircraft's fuel system then, yes, he can second guess the indication system and know that a fuel warning MEANS that something is not right and the warning should be taken notice of...
but I'm not talking about good aviator practice, I'm talking about a system component that seems to be sensitive to a water content in fuel that is below what can be detected by commercially available testing methods.
Why should a pilot have to be suspicious of a system's integrity and have to 'second guess' it because it doesn't do what it says on the tin. It should meet the criteria of its design approval under common circumstances. If it doesn't, then it should be improved to meet those criteria and at least have a maintenance/ monitoring programme put in place in the meantime.