I do not think that there is any difference between red diesel and the regular stuff. They dye it red so they can determine if someone (probably truckers) is cheating the system by not paying their road tax on the product.
I got behind the fuel truck one day and drove at 18MPH between the gas station and the marina. He had just filled the stations diesel tank. He then went to the marina and filled them off the same internal tank in the truck. The ONLY difference was he added a dye at the marina that he did not add at the station.... Off-road is dyed red and has no road tax but it is still more expensive at the marina than at the station.
On another note I often see folks using "Baja filters" and such. and I usually get a good chuckle. In Maine all stations whether on or off road are required to have filtering at the main tank end and also integral filters for each grade of fuel inside or mounted to the fuel pump. They are mandated to be changed once per year by law but they are also of a non-by-pass design so when they begin to plug the flow comes to a crawl. Usually they are changed multiple times per year..
At the marina we fill at most often they are using a 10 Micron pump filter...
My brother is friends with a "greaser" who owns an older 240 Mercedes and he once admitted that when he adds the time he has spent converting the car to handle "grease" and the parts costs, new fuel tanks, seals, pump, collection of the grease etc. that his cost per gallon is well over $10.00.. He freely admits he does it only because he's a die hard "green" guy and it actually costs him money...
Up here Bio Diesel costs more per gallon than #2 or street diesel...
I have seen and heard of far to many problems even with "blends" on marine engines. In cars the fuel rarely sits and the tank can be relatively clean, not so on boats, but still the greasers have more problems than they like to admit.....
I also think a lot depends on whether you get "home brew" or a good quality "refined" BD. The "refined" stuff is quite expensive up here..