Kathy, I believe that mainly it has to do with density and heat penetration. No thickeners or dairy should ever be added to home canned foods before canning. They increase the density of the product and may insulate it enough that some of the product doesn't see the necessary temps for the appropriate time when following tested recipes.
The way to work around that is to just add the flour or dairy upon opening. I do this all the time with broccoli and cauliflower I can from my garden. I'll can a thin soup, and then add the cream or thickener while reheating to eat. That canned cauliflower soup makes an amazing base for curries, by the way!
That same NCHFP link has great info on pressure canner use and practices, as well as safe, tested recipes for canning things like salmon and tuna. I do hundreds of jars of those each year, and they are wonderful.
Cooking on a crazy contraption...