Jose,
You are correct, the antenna on the keyfob is shorter than the one on the USB. This is done specifically to compensate for the resonant frequency shift due to the plastic encapsulation. The length used in the keyfob is specific for the keyfob with the effects of plastics and the hand taken into consideration. This length may or may not be the same for your plastic casing for your USB dongle. It could also be wise to make the antenna slightly longer and then tune the antenna by gradually reducing the length (it is much easier to remove length from a PCB antenna than to add it). This suggestion will of course require a PCB spin after the first production.
As for recommended guidelines for plastics enclosures, we don't have any particular documentation.
This link might be useful
http://www.kennethkuhn.com/electronics/rf_enclosure_design.pdf