It seems like I'm the one who usually breaks out the measuring tools and goniometer to assist persons in improving their fit, but now it's my turn...
When I set up my present bike, I recall using a goniometer to set the saddle height to right around 150 degrees between femur and tibia. I brought the bike in to the LBS right around that time, and never bothered to really scrutinize the settings.
In giving things a check, I discovered that my saddle height is about 1 cm higher than the most liberal of the analytical models.
This has not caused me any physical distress whatsoever over the past few months, and my power is good. My flexibility is also good, and I don't expect this to become a physical issue. However, I usually deal with saddles being too LOW, and now mine seems to be set slightly in the other direction. I realize that a saddle set too low will compromise efficiency. I also understand that raising the saddle reduces motion of the femur.
Am I losing anything in my case, or is it simply a matter of flexibility at this point? My usual references don't offer much insight on this side of the coin.