The herbies I have seen, all the emergency pipes are left out of the sump water level, including my tank. If it is submerged, it will be just as quiet as the main drain if you get a clog. The whole point of a herbie is silence, having a trickle in the emergency would kind of defeat the purpose, IMO.
I'd leave it where it is... and I would scrap the union on the emergency to, The emergency pipe is usually tall enough in the overflow that it only drains the for and inch or so (again, on the herbie systems i have seen).
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