because they didnt know how well the line would sell and designed them so if it got dropped by retailers, they could still release them in the cybertron line. and now they're being repainted and put in cybertron anyways.
They're being released in alternate colours in the last waves of Cybertron. That was always Hasbro's plan, I think. Optimus is based on his Universe colours (red ape) and Megatron is based off of Armada Predacon.
Errrr. Primal's recolor isn't anywhere close to the Universe red, green, and yellow. He's mostly brown and tan.
The keys were included in their designs so we could make dino anal rape jokes on message boards. And get surf songs from the '60s stuck in our heads when transforming the boss monkey.
Simple, Hasbro had some keys lying around and said, "Hey, why don't we give Primal a skateboard to use the key with while Megatron can do butt shots?"