For some weird reason my seatpost managed to creep down incrementally over several rides. I had not loosened it, so I had no reason to suspect anything was wrong. I just started to notice that the seat felt low. After a couple of days off the bike I hopped on to ride the morning commute and the change was finally obvious. I hoped off again by the side of the road, pulled the multi-tool out of my seat pack and raised the seat.
In the course of fine-tuning -- not to say fiddling with -- my position, I had made at least a couple of height marks on the post. Friction in the frame had obscured these scratches, but I could discern a couple. I chose the one that put the seat highest, about three millimeters higher than the other mark I could find.
Right away the seat felt kind of high, and slightly crooked. I have a lot of trouble lining my seat up with the top tube. That's one reason I purposely avoid messing with it, making a mysteriously loose seat binder even more strange. I figured it was good enough to get to work on.
On the ride home that evening I really felt the height. I felt knee pain, crotch discomfort, loss of power, and foot alignment problems. When I lowered the seat three (3) millimeters, all that went away.
The "science" of bike fit is complicated by the fact that humans are flexible and elastic and we fidget around on our bikes. Fit is not so much a matter of exact position to the millimeter, but rather finding the range in which a particular rider can operate most efficiently for their style of riding. In almost any dimension, most riders have a centimeter or two of leeway. However, as soon as you go beyond that range, you feel as if you're off by a huge amount. Thus I did not notice as the seat crept down, even as it crept well below the optimum position. I only noticed after I'd been completely away from the bike for a couple of days. Then it was obvious. Then, when I raised the seat again, I went that tiny bit beyond my functional range and started to feel all kinds of symptoms that might drive a less experienced rider to question multiple systems on the bike: cleat alignment, saddle choice or angle, and padding in the shorts, just to name a few. Yet it all stemmed from three millimeters of seatpost height.
The tiny amount, three millimeters, might seem to give some credence to the micro-engineering bike fitters. I say avoid getting too neurotic. Once I was back in range I could sit farther back on the saddle, which returned me to my familiar contact points. I could go three millimeters lower and probably feel fine as well. I just have an inferiority complex about my long torso and short legs, so I hate to bury the seatpost any more than I have to. Hence my choice of the higher height mark in the first place when I discovered the seat was too low.
The tiny increment does give you something to think about if you're chasing down an elusive lack of comfort or power.
Once you do get a position dialed in, measure every possible dimension to help you recover that position if the bike is ever disassembled or to reproduce the fit when getting a new bike. Pick measurements that don't depend on other things being equal between your old bike and your new one. For instance, if you drop a plumb line from the nose of the saddle to see how far it falls behind the bottom bracket shell, make sure you're using the same saddle on both bikes or have compensated for any difference. A wider saddle will put you in a different position, probably farther forward, than a narrower one. Measure every wacky thing you can think of before you disrupt the position on a bike that fits you well.