This is not always true, most line boring machines require two setups to complete the job and rarely do they end up perfectly in line down to the tenths like is possible with a line hone. Most aftermarket blocks are simply line bored from the factory and you can see the mis-alignment in the main housing bore by simply stroking the line hone mandrel through a couple times on low pressure. Just last year Dart had to start line honing all their new SHP blocks as part of the production process because there were too many complaints about mis-aligned mains. This is very apparent on motors where we are running less than a couple thou of main clearance as you can see the scrubbing on the bearings on tear-down of the motors that were simply line bored rather than a two stage line bore then line hone.
The change in crankshaft centerline is minimal, and almost always less with a simple align hone, if the caps are clipped .004, then after honing to size the change in centerline is about .002" - I have never seen a line bored block scratch in with less than that, usually it's about .005" with a line bore which is why all the performance timing chain sets are offered in (-.005)
Back to the original question, I always align hone these blocks with studs or stud/girdles because it's about 50/50 on the ones that you can measure a change or distortion in the housing bore, but an align hone assures you that all those main bores are perfectly in line with each other, something that takes as much time to measure properly as it does to correct.