The meeting planners do this so they can cross check names with hotel reservations against those registered for the conference. This is to ensure only those registered for the conference get the special conference rate at the hotel. Usually there are notes in the rate details, or other information if MR benefits don't apply or points can not be earned. I just booked a room through a conference web site for a conference I will be attending in July and within a few minutes the reservation was already showing under my reservations when I sign in to MR. As others have mentioned, there maybe some perks booking through the conference website. For example, by booking through the conference website, the resort fee was waived for my room.
If by Washington in April, you mean Washington, DC, be aware that is a very busy time for hotels in DC. Lots of tourists and school groups in town for the Cherry Blossoms and other events during that time. Room rates in DC can run double your conference rate during April, so whatever you decide, book early!
Regards,
RIP...