I don't have personal experience (yet - looking to build a box or get a Soundstream USB-8A or similar and put it by the spare as well) but I would expect that it would sound much better in the trunk. The flip up cover is thinner and more sound-permeable than your seats, which are super padded and will muffle output. The rear hatch will act as a natural acoustic reflector to add volume to the sound (the equivalent of "corner loading" a HT sub) and the sound will be more even throughout the cabin, especially in the front. If you put it under a seat it will be more localized and someone's butt will be vibrating constantly, plus rear passengers will probably kick it.