I wonder if this has to do with commissions? I don't believe that Disney would ever discourage guests from booking online (particularly as they seem to be constantly streamlining the process) or from calling with questions after doing so. In fact, many questions present the CM with an opportunity to upsell. However, if the CM's are paid commission, I can see that they wouldn't want to spend time answering questions about an existing reservation when they could theoretically be making a new one. Of course, answering questions is obviously within the scope of their job and they should expect to do so in a professional manner.
I had to call earlier today to upgrade our free dining reservation, and the CM made a comment about my having booked online. At the time I thought it was unusual because I never had someone comment on that in all our trips. Now having seen this, I wonder if the root of it is commission.