Building a custom box is a lot harder than it seems, and modifying a prebuilt one will most likely ruin it.
Go to http://jlaudio.com/tutorials/magic/index.html
for some great info on enclosures and in another place in the tutorial it talks about making a custom box and the variables you'll have to deal with.
I'd say stick to the one you picked out (or any other MDF box), avoid fibreboard or compressed pulp wood, or any light solid wood for that matter.
Make the LEAST ammount of holes in it (with screws or drills)
and don't even think of putting anything inside it....
If you're looking for space, try mounting the electronics on the roof of the trunk