If all things are equal then the sub location under the driver's helm is direct radiating and wins by a country mile.
The passenger console can easily attenuate the bass by 5 or 6 dB which means it takes four times the power and four times the excursion to get the same output. The woofer and amplifier operating most conservatively always sounds the best. With a large enough enclosure and larger woofer(s) and enough amplifier power you can engineer enough leverage to overcome the passenger console. But it will always be more of a boat shaker than a musical bass maker. Also, the altered phase response of the bass radiation coming from the passenger console will make it hard to have any degree of coherency with the midbass from the coaxials.
I would prefer a 10" direct radiating from under the driver's side over a 12" concealed in the passenger locker. In the end you will have to take what the boat gives you. Don't place a larger woofer into a mismatched enclosure just to force fit it on the driver's side. If you have to accept the passenger side then venting that compartment with a grill of sorts that has an open surface area at least equal to the woofer's surface area helps a great deal. No one wants to turn their boat into swiss cheese but tiny vents are worthless.
A high grade (absence of voids) exterior birch ply, MDO, or Medex is ideal. All solvent based versus water soluable construction. All should be exterior sealed regardless. Polyester resin is okay. Epoxy resin or professionally applied bed liner is better. MDF will work fine with the proper steps. I place execution as more important than the actual material used. In every case, you must elevate the enclosure up off the sole with polymer or composite risers/pads to allow for drainage and evaporation. Any enclosure will eventually fail if you plant it down directly on the carpet not to mention the mildew and mold trap that is created.