I've used Rodenstock and Fuji and both are excellent. I doubt you will notice the difference. I just attached a Schneider Componon-S lens to my friends enlarger who has been using a no-name plastic enlarger lens and even then the difference is minimal. When you're using high-end enlarger lenses such as Rodenstock, Schneider, Fuji, Leitz, etc. the big difference will be in HOW you print/enlarge/focus as well as the negative quality in question. I wouldn't worry too much about these lenses and would probably go with the Fujinon for the extra f-stop as long as it's clear of haze and fungus.
I notice you also shoot medium format. Why not dump extra money and get an APO 80mm or 90mm lens? That's what I chose to do and I just use my 90mm APO Rodagon f4.0 lens for 35mm and medium format. It's nicer to be closer to the paper with the 50mm and use shorter exposure times, but I'm okay with that.