That works well when the pipe goes in the top of the tank, but what about systems where the water enters from the base of the tank?...
You have a point.
However in that case I would recommend that the bulkhead fitting just be used to allow the pipe to pass through the side or bottom of the tank, and then run it up to the surface and then where you want it to come out. Drill your hole where it comes to the surface.
Of course, you could also reroute the plumbing up over the edge of the tank.
Check valves, any type, are just going to fail with all the stuff floating around in a reef system. I speak from experience. New, just installed, right out of the box they seem fine. A little later, and it sticks open during a power failure and you have a flood. Then the process repeats. You clean the check valve, test it, time passes, it sticks open during a power failure, and you have another flood.
Remember, it doesn't take much to keep the check valve from completely closing, and just a little back flow will cause a flood if given enough time.