If you have the choice, the cleanest installation when you are going to tile the walls around the tub will have you make some notches in the studs so that the flange will fit in and then be flush with the outer face of the studs. Then, when you install the cement board (cbu) with the vapor barrier behind it, it can be run down to about 1/4" of the tub surface over the flange and the vapor barrier without bowing out. The ledger boards help support the tub's edges and keep things level. They do not support the tub (i.e., it can't be hanging from the ledger boards). They only keep the edge from deflecting if you lean on it.
The mortar underneath the tub makes it feel more substantial, helps prevent stress fractures from deflection, compensates for an unlevel subfloor, and makes it last longer. There are various things you can use. Some people like stucolite, deck mud, but sand isn't a great thing because it will move.