I just bought a '96 SP (YIPPEE!) and the tag reads "SP-B28".This being said, there's a pretty good chance these number plates have no distinguishing properties at all, and were just pulled out of a bucket one at a time and riveted to the nearest triple. Considering you mentioned that you saw a 1996 SP with an E notation, it kinda puts that whole explanation above null and void lol. I'd find it pretty interesting to see a small sample of build years, vin numbers, and number plate numbers to see if there's any distinguishable pattern.
I can tell you that the 998R is not like that. I can tell you what VIN it is based on the number plaque.I'm pretty sure this is the way it is with virtually all Ducati numbered editions. Bike rolls down the assembly line, Giuseppe reaches into a box with numbered plates, grabs one and affixes it to the upper triple. The number you get is luck of the draw not a result of the effort it would take to match serial numbers with plaque numbers.
To put this into context, this is much better than in Ducati's earlier days when a fly might land on your fiberglass (a la Cook Neilson's Old Blue https://www.ducati.ms/forums/14-vintage/58016-fly-fiberglass.html ) or Giuseppe might flick ashes into the still wet bodywork and that's the way your bike would be "special".