Sometimes, moving the subs or any speakers for that matter changes/remove standing waves that would cause coloured quality. That said, I would highly doubt that your hatch is 'absorbing' much unless you have a bunch of carpet or cotton or sound absorbing materials in there. I would first check both speakers' polarity, loose mounting, adding sound deadening materials to the panels and hatch to eliminate the noted rattles. Additionally, make sure it is properly filtered with the x-over and driven by good clean power.
There are too many variables without knowing your whole set up, music, volume you are listening to, etc but I would think if you were to add sound deadening and have it properly powered and adjusted, it would make a whole world of difference in comparison to simply moving the sub since subharmonic frequencies are much larger than any car interior to begin with which translates to you already in the sound field. Moving the angle or source at these frequency rarely make a difference with the noted above exception. BTW, the there something call corner loading which works on the principal of horns. Having a sound source at a corner can enhance lower frequency. The Z hatch will aid this to some degree.
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