I saw that the amp was in that space, but by losing the cover, you can still save another 1" or so of space....although I can understand why you left it there since you'll be able to take the sub box out easily and have the whole cargo space to use.
I'm also doing my install and I've been looking for ways to have great sub performance, without using a bulky enclosure, while still maintaining all the usuable cargo space so I can go on vacation fully loaded without taking out the sub. The JL 103v3 was near the top of my list but it's total depth was greater then 6". Factor in the enclosure and grill and it will easily be 8".