I’ll be taking the Hong Kong Airport Express to Tsing Yi Station and then transfer to Disneyland Resort. Can I still board the complimentary shuttle bus at Hong Kong station to my hotel if I take the MTR from Sunny Bay to Hong Kong Station? All these are on the same day.
Assuming you are referring to these shuttles http://www.mtr.com.hk/en/customer/services/complom_free_bus.html the answer is probably yes.
I use them frequently and there is no kind of ticket or access control that I'm aware off. You just hop on at the hotel (or the station) and get off wherever you want. You don't need any MTR ticket or any sort of proof that you will use or have used a specific MTR train.