To get around the length limitation, you could cut the box in half. You'd have a little gap in the middle, but could use this feature as an adjustment for different length batteries.
Also, since the box is to encase lipos, I wouldn't use it as an ESC heatsink since that will just make the cells hotter.
Other than that, it's a good idea. It's just too bad they aren't a perfect fit so you don't have as much wasted space internally. If the body still fits, I guess it doesn't matter...
As far as the trays I make; they aren't that hard or challenging - just time consuming with archaic tools.
The benefit is that you can get an exact fit like neil stated. Some people even use hacked plastic trays from other vehicles, angled CF pieces (but be careful! CF is conductive!), angled Al, etc. You could even make fiberglass trays if weight is a big concern...