All the boxes I've seen for under our back seats take up the depth between the cubbies and the bottom of the seats. Idk about the factory sub enclosure. But in order to use the prefab boxes (Obcon, eBay specials, etc.) you have to remove the load flat floors for them to fit.
Here's a pic of the box I just had built..... fiberglass bottom and recessed subs. They're JL Audio 12TW3-D4's. 2 JL XD600/1 Amps push them. I haven't heard them yet (Truck is at home...I'm in Texas
) but tomorrow I'll be home and the guys at the shop said I won't be disappointed!