1. To obtain a rectangular cell, open Bulk Tools -> Supercell the Builder, change the crystalline system to "Base-Centered Orthorombic" and click transform.
2. You can use the "Swap axes" tool in Bulk Tools -> Swap axes
3. I guess this is because the rotated cell is not commensurate with the unit cell
To make an MoS2 device, apply 1. and 2., then repeat the cell along the C direction (Bulk Tools -> Repeat), then use "Device from Bulk".