To put a finer point on NuBu's comments, you have to have a 12-inch sub's surround 2 1/2" off the sole or you'll seriously choke it's output. You also need an inch minimum clearance between a vented pole piece and the rear interior of the box.
The JL Audio 13TW5 is a 13-inch with a mounting depth of only 2 1/2" and works in a .8 net cu. ft. enclosure.
The shape of a sealed sub box is of little consequence (as compared to a midrange) as long as the displacement is right. However, 5 1/2" O.D. might still be a little shallow. I'd use a 3/4" thick baffle and recess the woofer using a backloaded ring. I'd also use a 1/2" back with multiple stiffening braces. This way I could maximize my interior depth.