My thought is that this may have prevented the vent from opening when it should.
Nah. You're talking a fraction of an inch. If you're worried about the joker valve malfunctioning, just use a small open tube vented outside of the boat.
Recall that the siphon break works because it takes less force to suck air through it than it does to lift a hose full of water out of the sea. I can't see how moving it a half a hose diameter below the peak of the hose ID is going to make drawing air harder then lifting all that water.