If, Let's say, In Steam Vr Advanced Settings I set my height to -1. Would the run still be able to be submitted? It gives a serious teleport advantage and would cut down times by a huge margin. I don't see any rules about this, Is this allowed? If I only increased my height by, Let us say, -0.5, Would that be allowed?

This is a VR game so players of all heights play this game. I don't see a small height difference to lower times significantly. Obviously if there are altercations to the player via external programs the run will be rejected since it violates the rules.

what about standing on a chair or stool

Please be safe while speed running. Standing on a chair or stool sounds dangerous. If a player's height seems altered in a major way the run may be rejected.