Reason for the 335i hubs is to keep the 335i brakes. Otherwise you will have larger brakes on the rear than the front as well as them being designed for the M3 brake cylinder which is bigger. You could keep the M3 rear hubs but you'd need either M3 front brakes+hubs or a balanced front bbk.
As for the main driveshaft / propshaft, you do have a choice. Either 335i shaft from box to after the centre bearing, joined to an M3 diff end, OR an 335i box end joined to M3 shaft before the centre bearing. It's really just to ensure the length from box or diff is correct to the centre bearing mounting point, and that only one cut and join is needed.