There is this little thing called Transfer Function.
Basically when you put a box, your box, within another box, your car, the bass response changes quite dramatically. At a quess something like a 12dB lift at around 50-70Hz. This is an amazing thing as it can make a crap box sound louder.
When you put a box outside in open air with no surrounding walls, the so-called BRANDED boxes tend to sound really crap. I like this because I make boxes that sound good outside in open air with no walls because I know that when put in a car they are going to blow people away.
What you are experiencing is the fact that different cars generate different levels of Transfer Function and in some cars this can make a big difference to how two cars with the same equipment can sound so different.
I doubt your Dynomatt is making that much of a difference, what it will do is make the box ie your car, a bit more rigid and thus vibrate less and thus you hear the music rather than the box or your car. Incidently Dynomatt, contray to popular belief is not the best of sound deadening material and it most certainly is one of the most expensive. For those in the UK, there is a material that looks the same if not better, works better and cost 70% less than dynomatt and is readily available across the country from the "Brown Brother Motofactors" company.
When you put your seats down, you change the box parameters of your car, you also allow the air from the speakers to be coupled with the air in your cabin space, this will make the perceived bass in your car seem quite overwhelming.
Transfer function is what helps a lot of people create street cars that they think everyoone else wants to hear.
But remember this Bass can only be in one place at a time, do you want it in your car or outside, because when I drive down the motorway, I do it from inside my car not outside on a skateboard.
Enjoy your music, the 2nd gen MX6 sound good in any case, I brought mine almost soley for that reason.