Actually, as the OP states, the issue is with focal distance.
The military has been using AR/VR in heads up displays for decades now and have had to work around these issues. When a user is forced to focus on a 2d projection of a 3d field, it creates all the issues people have with VR including: vertigo, nausea, eye strain, anxiety, and malaise. Motion exasperates the issue.
The VR technology tries to eliminate any real world point of reference which makes us use reference points inside the VR which, I believe, is one reason the experience for us gets disconnected.
The most common symptom of this is that you get nauseous. My guess is that the (sensory) disconnected experience makes us lose balance.
What would solve this problem, I think, is to make the VR work with the whole body. So wearing a suit with goggles and standing on a plate that moves as you move which gets translated to in-game movement.