Not sure if this will be helpful for you or not... but here goes:
It seems I"m a little odd in that I balance on my tiptoe (of my unclipped foot, with the other clipped in at the top of the pedal stroke), still on the saddle, at stoplights instead of stepping down flat footed so my butt is over the top tube. I do have to lean my bike to accomplish this, and I guess it puts the saddle somewhere in between where it would be if I were sitting on it, and the crease where my leg meets my pelvis, if that helps you picture it. And yes, my foot/calf muscles do sometimes get a little tired, especially if the light happens to be on a hill. But it makes for a quick takeoff and it might solve your "hitting the top tube" dilemma, at least temporarily until you can get a better fit.
I don't claim that this is a better method, it's just what I ended up doing for some reason. Actually I think it wears my left shoes out faster.




. Actually I think it wears my left shoes out faster.
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