I would leave it alone to begin with. If you aren't happy with the sound, you could always add the ports later. I doubt there would be a huge difference either way. As an expensive and difficult option, you could always remove the rear deck completely and fabricate a new one...

One thing to consider, if you decide to go with a bandpass enclosure for your subs, you could always custom build it so that the port goes directly into the cabin via the 4.5" holes you mentioned. That way, all of the bass energy would be routed directly into the cabin, rather than being absorbed by the rear seats/trunk.