Lots of cars were "prototypes" or more actually one-off or limited -run "specials"; whateevr motor stuffed into whatever modified or cobbled-together frame (Cad-Allard, Cobra, Jag-Lister, Chevy-Lister—the list is endless .... )
---- In the day, prototype was far different from what you, probably correctly, call specials.
The FIA has strict rules for true prototypes which is why they had to have a spare tire and room for the official suit case etc .
Somewhere at the very end of the '50s (I forget which year than actual class was created) the reigning Euro sports car consortium recognized a class of purpose-built racing machines that were still both sports- (or GT) cars and also full-on racing cars. Jag D, Ferrari I think P-675 which begat the P2/P3/P4/512S/512M (Not using Google or notes here, just my porous and dishonest memory) leading to the Lola GT which begat the Ford GT-40 in its three or so variations, while Porsche built the RSK, then the 904, 907, 910, 908 .... Not dishonest just, not right and mostly wrong.
In 1962, the World Sports Car Championship was for replaced with the
International Championship for manufacturers of GT cars till 1965.
On a whole types of cars were rated in Groups of 1-9, if I remember correctly, though groups and group classification changed a lot over the years.
Over simplifying -- but here is the/a Appendix J classification that made prototypes, prototypes and not simply sports racers.
http://argent.fia.com/web/fia-public...1965%20ENG.pdf
Appendix J rules forced manufacturers to put I spare tires and a spot for a suit case.
Groups 2 to 5 GTs were what SCCA & IMSA sedan/gt classes were loosly based on.
There was no distinction between "GT" and "prototype" in races then—these were simply classes in multi-class races (Le Mans had about as many as the Nürburgring races have now, or more.)
-- That is not simply wrong, but horrendously wrong.
In the sports car mainstream, there was never a thought of dividing "prototypes" from other classes because they were still all just different classes. Once Ford and Ferrari (and Porsche) hit the class hard, there was no way to win overall in a sports car race without a hyper-advanced pure-racing prototype.
-- Get book a read some history.
Your story here is sounding too much like Moby Dick.
So at least part of the answer to why we see mixed grids would be, because it had always been done that way.
-- Wow, you are actually correct on that one.