Someone else may want to take a stab at your original question of whether it's necessary to flush-mount or not. My understanding is that flush mounting a driver will reduce diffraction of soundwaves. Diffraction off the edge of drivers have more impact on shorter wavelengths than long (ie more impact on high freq).Since we'll talking about the woofer, I don't think it's absolutely necessary to flush mount it. It does go up to 1600Hz, but at that point, the soundwaves are narrowed to approx 90 degrees and should not be affected by the driver edge.
With that said, you did mention you're building this out of solid oak, which means you're after a nice looking cabinet. Flush-mount drivers do give a speaker a more finished and professional look.
Gar.