I thought the vented loop you're talking about was only used for overboard discharge to prevent water outside the boat from siphoning back in. I believe the hose that fills the holding tank attaches at the top of the tank, so there's no way the tank can siphon back into the head.
A previous owner replaced the waste hose and bypassed the Y valve entirely on my boat, and plugged the overboard discharge. I'm pretty sure the head connects directly to the holding tank.
