Personally have never received any benefits associated with elite status when booking third party (except when booking with FedRooms). Occasionally, a hotel might make some things available when I bring up status, but this has been rare. For that reason, I almost always will book directly with IHG (or Marriott, or Hyatt, or Accor). YMMV, but I wouldn't get my hopes up too high.

I'd also take anything from IHG customer service with a massive grain of salt. It's my understanding that their customer service agents make Marriott's look good.