You're not going to have enough air space to push the speaker if you do it that way. Regardless if there is enough physical room to mount both the speaker and amp there, you still need to make sure you have enough air space to make the speaker sound the way you want. Another thought ... if you put a large speaker there, you will get a hell of a lot of door rattle and the system won't sound right. Even my system needed sound proofing in the side storage compartments (jack and spare tire set storage area) to get rid of all the rattles. My 12" sub hits really hard and is loud, but I have enough airspace in the hidden storage compartment to push the speaker.
Bottom line... you need enough airspace to make the speaker cone flex. I don't think the back hatch will do that for you, especially with an amp there as well. If the audio place is able to custom make a surround for the speaker and amp, it may work, but I doubt it. Plus, you will lose that storage amount as well. The speaker they have their now isn't a true sub. It is only a 6" speaker, so that isn't an issue with the stock system.
The deeper you go, the cooler it gets!