WeatherTech didn't make a one piece for the 2012 w/ the flat foot rest, so I had to go with the HuskyLiners which also didn't make a one piece, but they did make a center hump cover. It's not ideal but I made it work. If I knew this was going to be an issue I would have likely opted out of the manual 4x4 on the floor.
The shift lever trim comes up fairly easily. There are 4 "snaps" that need to be lifted straight up. Start w/ the passenger side, then the bottom is easy. Slide everything up the shaft and you'll see a 10mm head bolt facing the driver's side. Remove this bolt and everything comes off, simple. I first tried to trim the floormat, then install the plastic trim piece over the mat. The mat is too thick and wouldn't allow the trim piece to snap back in place. I ended up having to trim the mats to clear the plastic. I still recommend removing the shift lever and trim piece because it makes it easier to trim the mat. There will be a harsh outline on the carpet where the trim piece sits making it simple to cut the mat.
I still was able to get the flat, front portion of the driver's side mat to tuck under. All in all it's "OK" but not perfect. It will get the job done.
Hope this can be of some assistance to those of you w/ the shifter.