What did you end up doing? I have been doing a lot of homework and trying to decide between the Helix system, or a JL subwoofer (which omits DSP and cabin amp, but can be added later). I have a couple local Audison dealers who have a good deal on the Golf sub alone... (the entire Plug-N-Play system is about $2K, and as someone else said, for that kind of money, you can build a much better system). ...and one of these dealers is recommending against the Audison in favor of JL, at a much lower price. (I've never had Audison gear, but I had my 2006 Jetta TDI outfittied with Hertz speakers, and ARC amps, and it kept up in sound quality with my B&W Speakers and Integrated Amp at home).
That said, the JL Audio Sealed PowerWedge CS110LG-TW3 is only 4.5" deep (plus grille), and fits face down beneath the hatch floor (like the Audison Prima box, but much smaller). Totally concealed, and a JL JX250 amp is matched for it, and modestly priced for a decent mono-block. Another great option, is something like an ARC XDI 850.5 or Hertz HCP5D 5-Channel amp for both cabin speakers, and sub.
NOTE: If you are really on a budget, JL makes the ACS110LG-TW1: Single 10TW1 PowerWedge+ with DCD Amplifier. This however is about a quarter inch taller than the floor allows in the upper position...the hatch floor will latch snug, but sticks up a little on the sides (hidden by cargo block carpet).