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Action and intonation: which order?

The rule should be that yes, make sure your intonation is close before beginning a setup because why wouldn’t you want to be in the ballpark? Who wants to begin a setup if your E saddle is half a step out? We tune up before measuring relief etc, so intonation should be in the ballpark too.

Check it first, get it roughly in shape….Then do all setup steps first and then FINALIZE intonation last.

The above assumes an instrument you haven’t met before. If it’s already your instrument, presumably your intonation is close because you’ve set it before.
 
I’d agree with what’s been said so far, action first as the strings being excessively high or low will change the amount of intonation adjustment needed to correct the stretch as it gets pressed to the fret or fingerboard. Maybe not an huge amount of difference but there is some. Obviously there’s back and forth on all steps of a setup and once I finish one I’ll go back a day or two later and recheck everything.
 
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