Like anything tech wise, the devil is in the detail and how you set it up.
Most 3D capable TV's had at least some form of adjustment of the 3D effect, other TV's had quite a few options on tweaking the 3D rteplay.....it also depends on how close you sit to a 3D TV on just how good the effect is, and if you are viewing via a Passive or Active 3D.

You have the same sort of setup issues [measuring and setting eye to eye distance for each user] with the VR headset if you want to get the best out of it

It wouldn't effect anybody playing the VR version if the update also included the meta data/flagging for 3D TV's, it's just a added option that could easily made available for those who would like to use it, and don't have a VR headset.