I have good news for DSLR scanning stitching work, especially regarding the stitching of featureless areas. With a system that has excellent repeatability one can stitch an image that contains lots of detail throughout, hopefully arriving at a very low control point error value and save that run as a template in PTGui. From there you can open another set of images captured with the same set of values and choose 'apply template'. No control points need be generated for the new set. Choose the 'create panorama' button and done.

I played with this a bit and tried to break things and couldn't. If the replacement images are rotated or offset from those used to make the template you'll get a funky product showing such but the stitched output can only be broken by scanning with different stepping distance values or errors in repeatability due to scanner precision.

For a while I tried to use PTGui's 'replace images' feature but this was troublesome and in fact the wrong approach. Templates were designed to do just this and in practice they work beautifully. I would still advise control points be generated for images that aren't subject to orphaned images due to featureless areas, it could result in better seams along picture elements for one.