I don't see why not as when you check in they don't know how you booked - the only requirement is staying in one of the onsite hotels (or being a holder of certain APs)
You get all the perks associated with a Disney hotel reservation, regardless of how you book.
You need to show your Hotel Easy Pass to use EMH, which you will be given at check-in. I have booked some of my reservations at the Santa Fe and Cheyenne using an OTA and I can confirm you have all benefits of on-site guests!