I have a 2002 Chevy 1500 at work that needs the rear frame section replaced. Everything is pretty straight forward with doing the task, but there is one question I just don't know the answer to.

With the weight off the truck, rear springs disconnected, bed off, I would think that this frame would have to be welded on with the rear a little low. So when all the weight is on it, and the weight of the truck on the springs that the rails would be pushed up some. Is there any standard starting point? Or is there no need for concern. The measuring system we use has specs for the truck hanging on the frame clamps. These specs must not be very good if the truck is on the wheels, thus it sure must not be good if the thing is on frame clamps with the bed off and rear springs not attached.

Any thoughts?

I've done a few of these, I had the same thoughts.
Here's what I do.
Put the front wheels on level ground. support the
rear on jack stands at front spring mount.(frame should level)Remove the old section, slide new one in. Set the length and tac one side then the other make your tacs on the top out side edge of the rails. Now set the hight of the rear section And support it.Tac lower out side of each rail.
When you weld the rails make 1" welds at top,side and bottom of each rail.Check For plum, make alternating stich welds. Keep checking plum.

But do you set the height at the rear of the rails on spec or below to allow for frame flex when the truck is put back on it's wheels.

The fit from the bed to the cab would be critical relating to this spec.

If the frame specs are with truck hanging on the frame clamps which are at the front spring perch and front cab mount, I have to assume that with the rear end out and bed off these specs would be different.

I've always put them in level. The way the springs are mounted. The load is spread even on the rail. If there is a slight flex in the frame, The bed should fix it when you tighten it down. What measuring system are you using? Did your new come with the GM tech sheet? If not I can send you one.