String stretch is a huge factor and that is why nut slots benefit and on steel strings pretty much eliminate the need for nut compensation when you learn to cut the nut slots very low. The lower the slot without going too low the less string stretch.
It should be noted that where we fret makes a difference just like where the capo may be applied in terms of the distance to the frets. It also should be noted that how hard someone frets changes the amount of string stretch and the resulting note as well.
When I set the intonation on the guitars I set-up every day I try to simulate a moderate player in terms of how hard they fret and how hard they hit the instrument. If I know more such as specifically how the player plays I simulate that to nail intonation.
Also classical strings I can stretch them a mile and they will to a large degree revert so I stretch them at least 10 times each. Steel strings I stretch them too especially for gigging musicians and after two good stretches they usually have around 90% of the stretch out of them.
There is more, lots more a lot of subtile things that do impact what results such as the arc of a string over the nut slot, saddle, frets, how high the action is etc.
And one last consideration, the neck Peter IS moving and on an electric the trem may be moving. I can measure neck movement with a full step bend or more on many guitars and all these things are considerations in how and why we set things up as we do.
At some point it becomes knowledge AND feel, science AND art and that is why AI can go drink paddy water it will never get my job I have a soul....
Lastly it is a good idea for those like me asserting something to note, please if you are referencing nylon or steel they are two very different animals....