Scotchguard could work if you concentrated on the seams. The fabric itself has a PVC backing that makes it waterproof, however the seams are not taped and therefore are not waterproof. The reasoning behind this is stress internally to the jacket. If the seams were taped, the jacket would essentially act like a sealed bag of potato chips since it would be water tight (and therefore air tight as well). Putting your fermenter into the jacket would then put a large amount of stress on the seams and one could pop.
That's a real long winded way of saying yes, Scotchguard or other breathable waterproofing agent could work well on the seams, but still may be difficult to protect against 5 gallons of liquid pouring into the bag.