I'm planning a box for a trunk setup w/ folding rear seat. The subwoofer will be facing the rear and port at the rear or side, and enclosure moved as close to the cabin.

What is the rule on height and width clearance of the enclosure in relation to the rear deck and side panels? Is there supposed to be space in between? Can either be flush?

You would want at least the width of the port away from the side With the port.  Otherwise the other sides could be as tight as possible.

 

 

If not sealing off the trunk with sub forward and port forward, then I've had most best results sub back port back and box pushed closer towards the back. Just not straight against the trunk lid. That might ruin any cargo space tho.. and most times it's a trail and error situation.