I'm sure others can give a fuller answer, but I'll try. They are one offs (or very small run), which in America were known and raced as specials. Sometimes a successful prototype becomes a Sportscar - so for example the Ford GT40 MK1 started as a prototype and raced in that category then when the definitive design had been developed, the decision was made to produce enough (over 50) so that it could be classified and raced as a Sportscar - by which time the 7 litre MK2 had entered the scene and taken over the mantle of prototype.
Sometimes a car that you would think is a prototype turns out after further investigation to be a production sportscar - for example the D Type Jaguar, of which quite large numbers were made (about 70 I think).
The Cobra Daytona Coupe you might think would be a prototype because only six were made, but that exploited a loophole and was not a prototype as it used the chassis and engine from the Cobra and sufficient numbers of those were made for it to be classed as a sportscar.
In our Wednesday series we are racing cars which were not prototypes - although SMS categorises them as Vintage Prototype A. The rules were changed for 1968 reducing the maximum capacity of prototypes to 3 litres, but a sportscar of which at least 25 had been made (reduced from 50) could have a 5 litre engine. Porsche and Ferrari exploited this and at great expense produced the 917 and 512 offsetting the costs through sales to private teams. The Lola T70 which had been a successful prototype now became a sportscar as more than 25 had been made and the Ford GT40 MK1 suddenly gained a new lease of life as a result of the capacity changes.
Sometimes cars are really prototypes, but not classified as such - the Ferrari 250 GTO for example - Enzo got away with not making enough (39 instead of 50 I think), but having been caught out the organisers didn't let him pull the same trick with the 250LM. They made sure in future that the required number had actually been made.
This probably doesn't answer the question, but hopefully it does in some ways.