When taping cementboard butted against drywall, is it better to use drywall (paper/mesh) tape with joint compound or cementboard mesh tape with thinset?
Since you will put tile over the seam and also, I assume, thinset you should use screws and mesh made for concrete board.
The cement board and thinset may contain things which reduce efficacy of typical drywall screws, compound, and tape. Don't tape the seam until you're installing the tile.
Behind the cabinets you can use standard compound.