Depends.
Yes, most smiths will part off at least 0.100-0.250" off the breech before chambering, probably to make sure they are getting into clean rifling before they indicate the reamer. Some blanks are better than others, and a good smith hopefully knows the difference. Bartlein, for example, typically cleans up very quickly.
That being said, it usually is not a matter of INCHES unless it is a stock inletting concern (very real, by-the-by).
It can also have to do with needing contour left at the MUZZLE for thread shoulder. Depends on what the measurements were. Now a 5/8-24" on a 0.970 muzzle is about without reproach...
Measure with calipers and see how long the shank actually is compared to what you sent them.
If I am being very specific on what I need a rifle to be, and I almost always am, I will draft and spec what I need cut, and send the parts I want used. It works really well, and I simply say in my letter enclosure that anything I did NOT spec, to please use their best professional judgement for how it should be done for my needs of the rifle.
Using good smiths, I haven't had the first thing come out opposite what I sent. Same as pointing bullets to the right place, it may not always turn out exactly as I had hoped, but a good smith will deliver what is asked.
ETA: my guess is stock fitment.
-Nate