At this point I feel like I can confidently say I'm very happy with the route I went. There's never a point I don't have enough bass, and it's very easily adjustable with the knob by the shifter. The amp and wiring all tucks extremely nicely behind the rear seat, and although the sub is a tight fit it does not intrude much more than the stock subwoofer did.
For anyone wanting a sub that's almost identical in sizing to the stock Sony subwoofer the JL 10" sub in the matching wedge box fits almost exactly under the seat after comparing the dimensions to the 12" setup that I have. Obviously you will give up some subwoofer output with the 10" though. I do not think the slight bit of extra space it takes up isn't worth it though, especially with how ****** the stock sub is!
The 12" JL sub and box paired with the NVX400 amp and Focal front and rear component speakers makes for a nice setup. I may eventually replace the stock Sony amp/sound processor, but to make the most of that I would most likely need to change the headunit from the PX6, which I absolutely love.