What is the format and focal length of your lens? You spoke of your standardized print size of 6”. Is that width, length, diagonal? This information is needed so that we can figure the magnification and compare that to the useable range specified by the maker. Use a lens outside of its specified magnification range and the image quality might suffer. That’s not a design defect, just using the wrong tool for the job.
In making small prints outside of the recommended magnification range for the lens you’d customarily use, you’ll get better results using a shorter lens that covers the film and is within its specified magnification range.
Rodagons and CE Rokkors are both 6-element 4-group enlarging lenses capable of excellent results. I’d expect little if any discernible difference assuming that both lenses are clean and in good condition. I believe that the “CE” of CE Rokkor lenses designates “Color Enlarging” where it’s assumed that greater accuracy is necessary for good results with color printing as compared to B&W printing. At least that used to be a commonly held opinion years ago. I believe that the CE Rokkor enlarging lenses were made in 2.8/30mm, 2.8/50mm, and 5.6/80mm.
I find it difficult to access the optical performance of an enlarging lens by viewing small enlargements. Better to raise the head as far as you can for maximum magnification (within the maker's specifed usable range) and make a print—even a small one—of an important area. Do this with two different lenses you wish to compare to see if there is a meaningful difference. They will likely give similar if not identical results.
Here are a few opinions on the CE Rokkors.
Many of us have similar favorable opinions of Rodagons or any other high-grade 6-element lens.