You can route the speaker cutout hole and mount the driver flush if you want to, but there is no diffraction and no difference acoustically. Since the driver isn't seen, I don't think it makes any sense aesthetically either.

The cast frame driver is true enough that it make a good seal right against the wood, so you probably won't need a gasket underneath. If you find that you do, then use the O-Ring supplied with the driver or use some tar or silicon and run a bead. I prefer not to do this because it is messy and makes later removal awkward.

After you have assembled he speaker, run some music with good bass content and feel around the enclosure for leaks, including the edge of the driver where it meets the baffle. If there are any leaks, then you can go inside and seal it with silicon. If you've done a good job of making cuts and the driver cutout hole is round and properly sized, you won't have any leaks.