I think that it seals better with the wood because the surface is level. I have it just overlap right under my rim of the sub so it makes a clean finish.
The PVC drain pipe works well, but I did end up getting some flared ports but I bought the wrong size dimensions. I got confused and bought 4.25" wide flared ports and I haven't gotten around to make it fit. My box sounds fine for right now, infact there is too much bass for the daily driver.