re bars to seat nose measuring--I've often thought that this measurement is tricky because different seats must have different lengths, so logically this isn't a good thing to rely on. I tend to try to measure the distance from mid of top of seatpost, but admit that its not easy to get the same measurement each time.
Also of course, slight seat position differences in the rails would be another factor that would make this measurement vary a lot from case to case.
re being out of the saddle and knees being near bars etc--maybe because I'm used to it, but when I climb standing or sprint on my 54cm Tricross, I guess my knees are right up near or inside the drops, but I've never had a problem with it (hitting knees specifically) and I sprint very often on this bike standing and or stand climbing for short sections.
Maybe being slight helps with this, I dunno. All I know is that it isn't a problem ever, and I'm pretty picky about stuff when I ride, bike setup wise with how I interact with my bikes.
*Now I realize that having bar end shifters are a factor, and my bike has sti's. And while I've ridden a bar end shifter bike, I've never owned one.