not being real familiar with BB90, if it was my bike, I would expect (like most bikes I've had/worked on) that the crankarms should be equidistant from the stays, when properly installed. This is not hard and fast, but usually works out that way.
So, just to move my confusion forward another notch, I would measure from the inside of each crank arm (could be at the end, using a set of calipers) straight over to the stay. If each side is within 1mm of the other, then I'd prolly call it 'good' and maybe consider the implications of this 'design'. If the difference is 3mm or more, I'd think something was askew...
An email to Trek should give their perspective on proper installation of the BB 90 crankset. Or it might even be online in a tech manual ?