Help....yes, I've been reading the many many threads about A/T shifters
On a serious note it's about getting that that box lower. I imagine there's some way you could make some kind of depressed tray in your tunnel to kind of lower the shifter down into the floorboard a little bit and then cover it the top of it with a boot so it just kind of seems as if the shifter is coming straight out of the floorboard. Now on the contrary to that I put my wife's on about a 1-foot pedestal for drag racing. But I do understand the low-slung shifter you're talking about and I could see it again being done bye cutting a square out and then making a box that fits that square that drops down about two or three inches and puts the mechanism below the floorboard. Anyways just spitballing out some ideas.....
Of course this would all have to be relevant to where you comfortably like the shifter and how much room there is underneath the floorboard to the transmission the Driveline. But I'm sure some of that could be sucked up a little bit.