There is a theory about wave doubling when the subs are facing rearwards, but since bass audio waves are so long at very low frequencies, it may not even matter. The wave doubling theory is that the audio will reflect off the back of the trunk, and double up with waves being emitted again, making it appear in the cabin that the sub is louder. Depending on the car, frequency being played, woofer, and enclosure type, this may or may not be noticeable at all. Way in the back, out of the way and along with the theory, seems to be the best option.
Porting an enclosure relies on a physics mechanics called wave doubling. You will get much more output (SPL) at the lower end of the sub's frequency response, but with the addition with unwanted harmonics and 'unloading' the woofer at very low frequencies. Ports are created for specific lengths, so there's time for the sound waves emitted from both sides of the woofer's cone to 'double up' and become louder. This is how you "tune" a ported box to have its peak output at the frequency you want. Although this produces much more output, there's a cost of quality. At the beginning and end of each bass burst, there will be much less SPL being emitted since there is no other wave that has been created by the other side of the woofer's cone to double up with. You also have issues with port noise, a whooshing noise, flaired ports help to solve this but dont fix the problem entirely. As jllphan said, in laymenís terms, the system will sound more boomy. I wouldn't go so far as to say it's more "efficient," but in terms of making more noise, it gets the job done well.
You should port the box only if the speaker is designed for ports. If it's not, you can still do it, but the results can be a little weird.
As for woofer unloading, this usually only occurs at frequencies under 20 Hz, which isn't in much music at all. This is where the backpressure of the woofer isn't there anymore, making the driver's suspension much less springy, and allowing the risk of slamming the suspension or damaging the voice coil against the back plate from over-extension.
Just as a note: I hate Sonyís car audio equipment. Their woofer cones FLEX, their amplifiers have terrible harmonic distortion ratings, they just produce cheep, car audio equipment. The rest of their stuff isn't so bad, but their car audio department is horrid.