Pleased you solved the leaking problem. That is a real pain. I too had the problem with leaking holes through the bulkhead.
As to the check valves, first I am relying on those that appear to know, and they are as emphatic as I was.
But, based on my eperience with one way valves, they can fail. In non boating experiences, I have had experience with the flapper breaking, and it could get stuck in the line. I have had experience with them not sealing. I have had an experience with them not opening fully and restricting the flow.
Now, as for boating experiences, a bilge pump can pick up garbage (even with a strainer) This is particularly true when the cabin is awash and paper, food, whatever are floating around as a slurry.
If any of that stuff (even a relatively small particle - such as a piece of paper) gets caught in the check valve, good bye check valve.
Perhaps the best reason is that a vent does not have any of those drawbacks.
As to the vented loop, what i did to avoid the problem with the vent being under water when the boat is heeled, is to put the vent as close as possible to the center of the boat. My vent for the electric pump ( have separate lines for each pump) is mounted in the motor well. It is nothing more than a small hole in the highest part of the line (any outflow just goes into the motor well). You can further add protection by having the pump line cross over so it goes from the one side to the vent located on the other side.
The manual pump does have a check valve as a necessary part of the pumping action. It is not an additional element. My recollection is that the Whale manual cautions you about using that check valve as an anti-siphon device - but I may be wrong. My Whale manual pump also goes into the motor well and does not have a vented loop (but it does have a loop) because the outlet is above the cockpit floor draining into the motor well. The loop passes high through the bulkhead through a hole just below the bench.
Whale also provides extra parts in case any of those valves/flappers/whatever fails - so you do know they fail.