I think you should go ahead and have this noted on your reservation. Just keep in mind that your room will be assigned from the available pool of clean/ready rooms when you check in. The fewer room turning over the day you check in, the less inventory there is from which to fulfil your requests. You may be able to increase your chances by being willing to take a room assignment that is not ready when you check in, but may be available a little later in the day.
Another DIS boards member (and WDW CM) CDSTapisRouge has posted some of the best info about how rooms are assigned at WDW resorts. This really helped me to understand how the front desk CM & I can work together to get the room location we want. AllEarsNet also has a great write-up on how rooms are assigned at
http://www.allearsnet.com/acc/cro1.htm.
Here's what CDSTapisRouge had to say.....
"In general the only rooms that are pre-assigned are those that have medical needs requested and/or are traveling with another party (or have more than one room booked). The average reservation (even with basic requests) are not pre-assigned. The CM that checks you in will assign you a "best fit room" when you arrive at check in." 5/1/06
http://www.disboards.com/showthread.php?p=12509273#post12509273
"...Disney does a first come first serve type room assignement unless you have a special need. The only thing that we pre-assigned where medical needs, rooms guaranteed for special needs (ie: non smoking due to medical, first floor for medical, things like that) as well as reservations with more than one room and/or a request to be near another party. Other than that a basic request like "near food court" would not be pre-assigned, if it was avalaible at time of arrival then they will assign it to you.
As far as the CM's on the front desk that actually check you in, there are a few different ways for them to find you a room. They can just change your reservation from guaranteed to inhouse and the computer will assign a room automatically that is clean and ready, OR (and this is what I always did) they can go into the full room avalability for the day and find a room for you. Now they can look it up by only room that are clean at that moment, or they can look at all rooms, clean or dirty, that will be avalaible that day. This way they can pick what room you are going into based on your requests vs what will be avaliable. But to answer your question yes...the room assigner does really exist, but they have a lot more responsibiltes, not just assigning rooms." 3/2/06
http://www.disboards.com/showthread.php?p=11737140#post11737140
...the scoop on connecting rooms...4/13/06
http://www.disboards.com/showthread.php?p=12276085#post12276085
...how DME & check-in work...3/3/06
http://www.disboards.com/showthread.php?p=11750527#post11750527
Good luck!