Actually they can. I am on a 3 week award stay right now, 2 of which were travel packages and they were linked just fine. No problems checking in, no extra points taken out. Now I did call back in November and had them connected to my award reservation. Certificates don't automagically get connect to reservations, you have to call and have them do it.

I also have two upcoming stays with Travel Package hotel certs attached to them. I also had to call to get them to attach the certs. When they did, I noticed that the hotel reservations, which I had made online, were slightly changed. The online tool now stats that I can no longer modify those two reservations online.