I'll take a crack at it (someone correct me if I'm egregiously wrong).
1) top tube is measured from where it meets head tube to where it WOULD meet seat tube if it were horizontal
2) the reason this effective length is LONGER than actual length is that BOTH the down tube AND the seat tube have slope. Put more clearly (I hope), if the downtube had slope but the seat tube were perfectly vertical, the actual tt length on a bike with a sloping tt would be longer. But while the down tube slopes away from an imaginary vertical line bisecting the bottom bracket, the seat tube also slopes away, in the opposite direction, so as you move UP the seat tube (=as the tt gets more and more horizontal), you are effectively stretching the tt out (b/c the sloping seat tube moves farther and farther away from the imaginary vertical bisecting the bottom bracket as it goes up). I checked this out on my new compact frame and I think it's true. But I'm not mathy (my verbal SAT score was several hundred points higher than my math score
), so someone go ahead and lay in if this doesn't hold water.
3) standover -- I wonder if this varies by manufacturer? I just measured my new bike, and standover ranges from 71cm at the seat tube to 75 at the head tube. The Scott website lists it at 73 cm. This seems to be the median? If you look at the geometry diagram here http://www.scottusa.com/us_en/category/72/contessa_road (you may have to click on the "geometry" tab), it appears they take the measurement somewhere in between.
Hope that helps, and hope someone can correct any major errors I may have made...




), if the downtube had slope but the seat tube were perfectly vertical, the actual tt length on a bike with a sloping tt would be longer. But while the down tube slopes away from an imaginary vertical line bisecting the bottom bracket, the seat tube also slopes away, in the opposite direction, so as you move UP the seat tube (=as the tt gets more and more horizontal), you are effectively stretching the tt out (b/c the sloping seat tube moves farther and farther away from the imaginary vertical bisecting the bottom bracket as it goes up). I checked this out on my new compact frame and I think it's true. But I'm not mathy (my verbal SAT score was several hundred points higher than my math score 
...
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