Exactly 100% spot on.. When running an open breather system, the factory PCV system has to be completely disabled, otherwise it will allow un metered air to enter the crankcase, causing a huge vacuum leak leaning out the air/fuel mixture.. I know this through personal experience which is exactly the reason I use an oil cap breather with a built in one way check valve along with my UPR oil separator that also has a built in one way check valve as well..
The oil cap breather functions just like the stock oil cap in which the check valve remains fully closed during normal driving conditions while the PCV is under vacuum and then opens up at full throttle when the PCV closes in order to allow the crankcase to ventilate..
Between both the oil separator and one way check valve breather, I can keep the factory PCV system fully intact without crankcase vapor oil entering through the intake manifold and then back into the crankcase..
The reason your passenger side blows out more vapor than the driver's side, is when the factory PCV system is disabled, your intake manifold is capped off and no longer able to pull vacuum out from the driver's side valve cover..
Therefore it's looking for the closest outlet/route for crankcase oil vapors to escape from which happens to be from the passenger side valve cover..
This is why it's recommended to use an oil cap breather that includes a one way check valve, as this provides you with 3 outlets for crankcase oil vapors to escape from rather than from just the driver and passenger side valve covers..
As for connecting the breather can back to the intake manifold with a one way check valve in place, may work.. However it won't prevent the vapor smell from entering the inside of your car through the air vents.. You might just as well be far better off by just keeping the factory PCV system active and run an oil separator/catch can that includes a built in one way check valve along with an oil cap breather which also includes a built in one way check valve as well