PROFILE IN A LOOP

If you're using Find Nominals, then yes, it will compare against the CAD surface it was defined on.

If you're looping parts (rather than features on a part) there's a technique you can use to make sure the model moves with the part.  The standard LOOP command doesn't work in this instance.

Use a do/until loop and recall external alignments for each fixture station, then saving them as curr.aln, then recall curr.aln before the part measurement.

If you're using Find Nominals, then yes, it will compare against the CAD surface it was defined on.

If you're looping parts (rather than features on a part) there's a technique you can use to make sure the model moves with the part.  The standard LOOP command doesn't work in this instance.

Use a do/until loop and recall external alignments for each fixture station, then saving them as curr.aln, then recall curr.aln before the part measurement.

That sounds like waaaaaay too much work. 

It's like anything, once you've done it a couple of times it's quite straight forward, or you can copy-paste a previous program (and simply edit where necessary).