Best advice is to visit our friends at the tile forum, www.johnbridge.com They are really good.
Just for discussion, I would offer that there is not necessarily one right answer. I would use mesh tape and waterproof joint compound. You may be able to use regular tape and joint compound. I would not use thinset.
I believe that for areas not actually in the shower, you can use mastic or thinset on greenboard or hardibacker.
That's my two cents. Check the forum I mentioned for more complete advice.