The bypass is a nice idea, but it makes the CAI redundant as it loses vacum and sucks hot engine air as it is open all the time.
If you are worried about a major rainfall ,pop the pipe off at its joint.
If the AEM is made of 2 peices like most them it should be abel to take a bypass of 3inches, unless they never thought of the room needed to be taken up by the bypass. In that case just shave an inch or so off the end.
Remeber it is not really a valve as nothign open or closes.
It is a strip of foam filter which normally sucks air in as a secondary but when water begins to be injested the weight of the water causes the natural gravity to vacume the air form the engine side of things.Problem is it takes large amounts of water at low speen for this to work.If you are moving at a high rate of speed and plow through a deep puddle the water gets forced up the intake anyway , and .............................bye bye engine anyway as no bypass can do anything about that.