Hi remoandiris,
At the Goshen Rally I talked with the Lippert Engineer who developed Correct Track to find out about this very question.
The theory behind it is that the weight of the trailers is not evenly distributed; partly due to slides and other design choices, and partly due to your stuff. The weight differences cause different compression on the springs. Since the springs are anchored to hangers at front and rear, the difference in compression may cause the axle spacing to be different on one side from the other.
I asked when the alignment should be checked, and he was specific that it should be checked when you're fully loaded in the way you would actually pull the trailer (including holding tank content). Doing it at the factory was not his recommendation.
I had been under the impression that the factory build differences would be most significant, but our weigh-in results seem to contradict that. Our Landmark is carrying almost the same weight on each side - about 150# difference. The laser alignment check showed that the axles were off by about 1/8", which is less than the minimum adjustment of the Correct Track system. So the alignment check seems to match the weigh-in results.
Just to make sure, after leaving the rally, I checked the trailer and truck weights at a CAT Scale to see if they matched the weigh-in results. Less than 50# difference on each, relative to the rally weights. So I have no reason to doubt the weigh-in results with respect to side-to-side weights.
The alignment check as Lippert designed it involves anchoring a shaft to the kingpin. A laser pointer/distance reader is mounted to the shaft. They have a reflector that gets placed against the tire, which gives a consistent target to measure against. The low-tech version of this would be to start with a plumb bob to mark a spot on the ground directly below the kingpin, and then use a string drawn tight to determine the distance from that mark to the front of the tire.
My conversation with Lippert's engineer, combined with the results on our Landmark lead me to believe that checking alignment when fully loaded is the correct way to go. If it were aligned at the factory, without your stuff, when you added your stuff, it would likely be out of alignment.
And of course most RVs on the road don't have Correct Track and do just fine. This is just one more tool at your disposal to find out if you have a problem and to correct it without major surgery.