Richard -- While a slight loss in grain edge sharpness is noticable in many focusing aids in the center of the image when stopping an El-Nikkor from f/5.6 to f/8, it isn't conspicuous in prints.
There often is a difference between the focus plane in focusing aids. Perhaps some aids are designed to be used on the bare easel while others are intended to be used on a piece of paper the thickness of the photo paper. The difference is inperceptible to many of us. Sloppy manufacturing and user maladjustment can also cause errors.
The purpose of aligning enlargers is to make the image on the easel as sharp as possible from corner to corner. Several methods of checking this alignment use indirect and artifical ways of achieving this. It doesn't matter if the film, lens board, and easel are perfectly parallel as long as the image is sharp from corner to corner! To check this in a condenser enlarger, I lightly abrade one surface of a piece of clear film with both coarse and fine sandpaper. With the lens aperture wide open, all corners of the image should simultaneously become sharp as you focus. If so, enarger alighment is O.K. If not, some enlargers have adjustments to correct the problem. Also, the negative carrier can be shimmed with tape to fine tune the alignment. When all four corners of the image are sharp, the alignment is good and the center should also be sharp. If the center is unsharp, it may be due to film buckling. Your glass carrier will solve this problem. Some cheap lenses do not form a perfectly flat image. In this case, stopping down may let them be used.