It isn't the service that is different, it's the policies. The key to making your reservation isn't who you talk to, it's what you want. Let's say you are looking to book a room only reservation.
WDTC CM's will automatically book you as a WDTC Basic Package which will include the room and an admission to either WWoS or a round of mini-golf. This will come under the regular policies of WDTC - $200 deposit, balance due in full 45 days prior to arrival, and varying cancellation penalties after that 45 day date.
But you can ask that same WDTC agent to have the same reservation made through CRO. You will then get a room ONLY, no extras. But you'll also get the balance due at check in and up to 5 days prior to cancel with no penalty.
If you are using a code (CFQ, ZBTW, etc.) or a DC discount when booking, then you have no choice in who books it. It can only be booked one way. You can beg, plead and cry but you can't change it because it's only available in the computers one way.
Bottom line: room only reservations can be made through either. You just have to ask for it to go through CRO if that's what you want. Codes and packages are not as flexible.