Hmm, I don't know if the direction will effect trunk rattle, but I could be wrong. As you stated though, you will probably hear less bass with this setup. I currently have subs facing towards the rear with a "ski hole" I cut myself and they sound great.
An aftermarket headunit will definately help your bass sound better. Not necessarily louder, but better. I don't think the stock unit sends out as low of frequencies as aftermarket units do (so it may be a louder at the low, low end), and you have no way to control your sub volume, unless you have a wired remote from your amp.
I ran the stock unit with subs for a little while, and it sounded ok, but the flexibilty of an aftermarket unit was definately a great improvement.
Additionally, I sold my old Infinity Basslink to a friend of mine who mounted it facing into the cabin through the "ski hole" of his BMW and it sounded terrible. I had it mounted under the rear shelf in my car, firing upwards and it sounded great. I don't know how much this relates to a traditional subwoofer setup though because the Basslink has a powered woofer on one side and a "passive radiator" on the other side, so the placement effects how the sound waves from each interact with each other. Thought I'd mention it though.