Hi Bernard,
If your Photorag papers are of matte surface and referenced to a Canon Matte Media Type, CO does not coat the paper surface so there can be no issue of gloss differential. CO only coats PK papers, where you have two options: total coverage or default coverage. The default covers all areas of the print where there is some ink density. So depending on the angle at which you view the print, you could perhaps see some difference, as only highlights would remain uncoated. Looking at prints from normal viewing angles there is no problem. If you use total coverage it consumes a lot of material for no good reason. Be aware also that the Canon Pro-4000 has no straight through paper path, so you cannot use it for printing on inflexible media.
You may wish to look at my review of the Canon Pro-2000 (same printer but 24 inch) as well as Keith Cooper's review of the same printer. Between the two reviews you will have a quite comprehensive understanding of how they work. I think they produce excellent prints and have numerous attractive features.
Cheers,
Mark