Sidetrack,
The Y-valve already installed on the boat is behind the holding tank.
It's purpose is to send the stuff from the holding tank, either over the side thru the macerator pump, or, to the waste fitting on the stern of the boat if you intend to have the tank pumped out at a marina or fuel dock. Either way, the stuff goes from the head to the holding tank first.
If you wanted to bypass the holding tank altogether, you would have to install a second Y-valve between the head and the holding tank. This Y-valve would allow you to divert the stuff over the side instead of letting it go to the holding tank.
In addition to the Y-valve this would require installing a thru hull below the water line and a sea cock, the same diameter as the outlet on the Y-valve. This would be a pretty big project. Just the parts are going to set you back about $300.00
Or, if you REALLY want to bypass the holding tank, just plumb the head directly to the sea cock and thru hull mentioned above, and forget about the Y-valve. However, this option is almost certain to get you in trouble with the law if they board your boat and decide to check if your plumbing compies with local statute.
However, this might hot be necessary unless you are going on a cruise to Tahiti.
There has to be a problem with your plumbing that is allowing fumes into the boat.
I have never used any chemical in my holding tank and have never had any problems with odors.
My guess is the vent line going from the top of the holding tank to the vent on the stern of the boat, is not connected. This is is allowing fumes from the holding tank to escape into the boat instead of going out the vent on the back of the boat. A leak anywhere else in the plumbing from the head to the holding tank would allow waste into the bilge, and you have not mentioned that waste is present in the bilge.