Well, the 3 speed is rare but this is one of those cases where rare doesn't mean desireable. A 3 speed car will take a hit in value over a 4 speed every time, all else being equal. However, if I had one and the numbers matched along with documentation that it was born that way, I would leave it alone. I never understood why anyone would order a 3 speed in a 1964 to 1969. The price difference is so little that if you could afford a new Corvette you could afford to order it with a 4 speed. Granted, some 3 speeds might have been built due to errors on the order form or maybe no transmission was even checked on the order form so it was built with the standard trans, the 3 speed. It couldn't have been an insurance issue because it is still a Corvette.
I'm sure that some 3 speed cars were ordered intentionally but I don't know why.
Tom