The scale length of a string is the length of the string available to vibrate, period. Sometimes physics disagrees with guitar lore, and this is one of those times. Yes, the scale length is a bit different on every string, which drives some people crazy.
IMHO, the scale length of a particular guitar is the distance from the saddle side of the nut to the nut side of the saddle, taken at the midpoint of the nut and midpoint of the saddle. It is a reference number.
So, in designing a guitar, you choose the scale length, which is used in the calculation for fret locations. Then somewhere down the line you compensate the saddle, to get the tuning more exact...which alters the scale length of those strings...which means you should recalculate the fret positions, which means you should....keep chasing your tail.
Guitars are not exact instruments in terms of tuning. Capos and even forming chords with your fingers result in pulling strings out of tune.
But like the bumblebee that theoretically cannot fly, some guitars still sound good to our imperfect ears, anyway.
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Angie
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