Other way around, if you delete the PCV valve but still plumb low side to the manifold then yes the flapper must be deleted too. Otherwise too much vacuum is drawn on the crankcase and you'll get a whistling sound from air getting drawn through the seals in off boost situations. You'd still need a check valve on the lowside otherwise boost would be sent straight into the crankcase.
Since VT still has a PCV valve on the low side, without the flapper the crankcase would see minimal vacuum but no issues should arise. Think of it this way - you have a sealed bottle with two hoses coming off, bottle representing the crankcase. If you suck on one hose (lowside to intake manifold), unless you plug the second hose i.e. the flapper valve's job, the bottle would see minimal vacuum since air would flow in through the second hose.
Only in off boost situations, once there's positive boost the PCV valve closes and nothing is drawn from the valve cover into the manifold. Catch cans are not 100% effective so vapor could still make it back into the engine in certain situations. I agree with Omar that preventing this altogether is better for performance.
How old are the plug and coils?
Precision Raceworks Coils less than a year old. Plugs NGK two step colder at .022 gap less than six months old. These are the things I am about to do this Saturday which MIGHT fix this issue:
1. Change the two idle pulleys (not tensioner pulley) - I noticed the idler pulley right in between the Crank Hub Dampener and the Tensioner Pulley Assembly is physically oscillating at an angular manner causing the belt to move forward and backwards to the front and rear of the bully edges - imagine the belt travelling towards the direction of the rear of the car and then returning to the direction of the front of the car. I don't know if this pulley oscillation and belt motion is contributing to this stop light idle oscillation but in any case, the pulley needs to be replaced since it is oscillating physically. I never seen this on my car before.
2. Change driver side mount from Black Forest Stage 1 mount back to stock 335i motor mount (and use the stronger passenger side mount in place of the driver side to have more strength - normally, driver side mounts are not as strong or expensive as passenger mounts due to the fact that the forces mostly go to the passenger side when revving.)
3. Change steering pulley to aluminum billet pulley.
4. Change sparkplugs if needed upon inspection and try NGK two step at .020
5. double check ALL vacuum hoses... perhaps there is a loose connection somewhere.
MHD resetting all adaptations on the menu did not solve the issue. Car runs fine, but this idle issue is noticeable and I know not to ignore 'new' sounds when they arise. I will keep working until I find the culprit. Just like the alternator pulley was damaging my serpentine belts consistently, so too I will find out wtf is going on here.