It is assembled correctly. It will only fit one way
It doesn't stick out further from the bag frame, but at a point about half/two thirds way down it's about the same outside dimensions. The steel cage just extends down where the bags do, but it's now one unified space in there all the way down to the bottom of the hopper. You will still have to clear past the obstacle you could potentially turn out (in) to, or yes, your rear end will swing the MCS out and hit what you don't drive/clear past. I don't think it's any more trouble on an "outside dimension" basis, but the MCS hopper extends lower below the frame and just inside of the 3 bag rig and cover. The metal casing doesn't give like the bags do.This thread got me looking at the 14 bu hopper again. I already have the 3 bag MCS with the Powerflow blower on my X754 so I think the dump from seat hopper would go right on with nothing more needed. This might be the year. Dumping those heavy bags is getting mighty hard on my old shoulders.
I have a 2025R with a loader so getting the grass pile stacked up after the mowing is done wouldn't be a problem for me. I am wondering if you could look into putting a front blade on your X739 so after dumping the hopper you could turn around and shove the pile where you want it. With your 4wd it should work easily and maybe even be kind of fun. I think you also have 4 wheel steer so maybe the blade on the front would be too much in the way and limit the effectiveness of the tighter turns.
That brings me to another question. Does the new hopper stick out further back than the bag frame enough to cause more trouble when turning next to fences or buildings? It seem I am always banging the hopper lid into something because the all wheel steering throws the rear end out when I make a sharp turn.