Phewy, the frame "size" is many times irrelevant. The big things are the effective top tube and seat height. Get the smallest frame you can get being comfortable on the handle bars (reach) with the seat at the correct height. (e.g. back angle 45, leg slightly flexed with heal on pedal).
I'm ~6 but wear a 31' inseam so I tend to get biger bikes then stores would recomend (21, 22, 58/59 road) because I'd feel cramped (e.g. too upright) on a smaller frame. (it helps that I'm reasonably flexable) However I tend to do heavy XC so I like being a little more streached out as well.
As for standover I've got about 0.5-1' clearance between my sit bones and the top tube (my front rests) and I haven't had a problem with croch checks. The few odd ones I've had were due to poping out of my pedals on a sprint, in which case I'd need like 4' of clearance.
That being said, if you've got a shorter torso then mine I'd check the M 19.5 (or even 18). From the Trek specs for every inch of stand over you gain you'll loose a little less then an inch of reach. If it's a decent shop they should swap the steam out to fit the bike to you. Usually you can fugde a stem enough to go to the next size down.