Making the claim that "it is still something and that something I simply don't want" is not evidence that the breather system will ever have a negative impact on the engine. And there is still not a shred of evidence that you are concerned about anything that is grounded in reality.
The fallacy you present here is that all cars are basically the same, ie, if one cars breather system causes soot build-up on the valves, then all cars breather systems will do the same thing. There is no evidence the CX-5's breather system will harm the engine. None.
You are assuming two things here:
1) That by modifying your CX-5's breather system the valves will still look new after 50-200,000 miles.
2) That a new looking valve with 50-200,000 miles will be better than a valve that does not look new.
But what actually matters to the performance and reliability of the engine is the functional condition of the valve, not it's appearance. And I have no reason to believe that a valve operated in an environment without crankcase vapors present will help the valve last longer or stay in better shape. Any oil vapor that may be present, could actually protect the valve and valve guides from wear.
I think I'm getting what you're saying. If you don't open something it will stay in it's original condition better. And that is the advice I would give to you regarding your intake manifold - don't needlessly break the factory seal between the intake manifold and the head.