i came very close 2 times doing that. so the thrid mdf box i built for my car was built inside my trunk. lol
have you tried this, remove the trunk floor board, remove the spare tire, remove the trunk lock latch, remove the trimming all around the trunk opening.
then slide the box in LONG ways. hopefully it will slip into the crater where the tire would be. at this point a smapp portion of the box should still be sticking out. well, here you have to push the box out a bit, enter the car and from the rear seats take the box and start turning and twisting it. you may be able to get it in.
question, what car is this and can we get pics of the opening and the box?
If done properly, it wont leak. You would need to make a clean cut, then use cleats inside the box. say 2" on each side off the cut. glue and screw one side on. let dry. then assemble the box in side the trunk. Just as jour sliding it together, load the seam up with glue. join it, and screw it. then after its dry, caulk the seam from inside thru the sub hole. and bondo the seal outside. its a lot of work, but it can be done. Im not talking about using a jigsaw either. Like laying the box on a table saw and talking 3"-4" inches off one side to get it to fit.wtf talk about leaks galore.
...?Wait until Winter. The metal that comprises your car will expand in the cold and you will have moar space.