Have you tried balancing it yet. Granted on my older alpha Ive convereted it to a tail dragger and its had some repairs to move weight around but when I balanced it I had to move the battery forward of the "battery tray" and only my reciever is in the battery tray. Just cause they say thats where the part goes doesnt mean it has to. You may have to move pieces anyway even if you stuffed the reciever and battery in that tray. But like others said the reciever can easily be moved to the side wall or elsewhere as its probably much lighter than the battery. And Using the larger battery it may be necessary to move the reciever back to balance out a heavier battery up front. And If you have to move it its pretty simple to make a brace with some scrap balsa / ply and foam padding.

From the pic it looks like you could easily fit the reciever in the gap between the battery tray post and the servo tray, leaving the whole battery tray for that bigger battery.