You're saying that the head discharge line and the tank pumpout line are the same line???
If so, that's NOT how it should be plumbed! And, if so, that needs to be corrected!
But I doubt that it is. I'd bet money that you also have a blocked tank vent.
The only purpose for any y-valve in the line from the toilet is to provide a choice between flushing into the tank or flushing directly overboard...it should have nothing to do with emptying the tank. If the tank is plumbed to allow dumping it at sea, the tank overboard discharge line prob'ly uses the same thru-hull.
So yes, the y-valve would have to be open to the tank to move waste from the toilet into the tank...but it should have nothing to do with dumping the tank or pumping it out unless you also have a blocked tank vent...in which case, the suction from the onboard discharge pump or marina pumpout would pull air from wherever it can...in your case, the toilet. The joker valve in the toilet discharge is prob'ly so worn out that the pumpout can pull in enough air through it.
But the tank vent should also provide an escape route for air displaced by incoming waste...if the air can't out, the tank will become pressurized, at the very least causing waste to back up into the toilet...worst case, a burst tank.
So your tank vent AND your toilet are in SERIOUS need of maintenance--and MAYBE re-plumbing...'cuz since holding tanks are not requred in your waters, it is possible that a PO installed your tank incorrectly. If you'd like to email me, I'll be glad to help you sort out what you really have and what needs to be done to make it right.
Meanwhile, I suggest that both y'all check out the link in my signature...it goes to a comprehensive "marine toilets and holding tanks 101" manual that will teach you how to install, operate and maintain your systems correctly to prevent 99% of problems.