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Action and intonation: which order?

In cases where very low action is desired, end of setup intonation adjustments could become noticeable in the action.
Maybe. I've run very low action in the past, and still never experienced this on properly built instruments. If the saddles have to be jacked up high to achieve the desired action, then adjusting intonation may affect the action, but they'd be pointing significantly upward. So maybe it "could", but it definitely shouldn't.
 
Changing intonation DOES change action but the change is not significant. It's very simple geometry. Moving a saddle plus or minus an INCH from its initial position to vary intonation will change action at the 12th fret of a typical 34" scale Fender by 0.004"

Realistic adjustments result in far less change.

In my experience a setup involves multiple iterations before things "settle", it's something I can do once and it's done.
 
In cases where very low action is desired, end of setup intonation adjustments could become noticeable in the action.
Please explain how. You are not changing the amount of relief or the string height. What part of the action changes?
 
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Please explain how. You are not changing the amount of relief or the string height. What part of the action changes?
When you move the saddle, you change the angle between the fretboard and the string by a tiny amount. That influences the distance between the strings and each fret, with the effect being greater the further up the neck you go.

Now, whether this is noticeable… I’m not sure about that. A quick calculation tells me that moving a saddle 10 mm forward would result in an action change equivalent to raising the saddle approximately 0.05 mm. So that’s 1/20th mm for quite a large movement of the saddle. I’d say that is negligible. I don’t think I ever make saddle height adjustments that are so small.

In practice, whenever I move the saddle forward, I check to see if I can lower the saddle height, and I often find I can. So… maybe it does matter? Or is the neck still adjusting to changes in the truss rod/string tension? Or maybe it’s some kind of placebo effect? I don’t know. I keep usually keep tinkering with my setup for a few days anyway.
 

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