Just wish the had a scripting command like phent_sethumanoid (myplayer); to tell the engine its a biped and to set the gravity properly.
Gravity has nothing to do with this. But you are right, you either use the physics engine and abide by the physics law (which is why I suggest changing the bounding box so you are not breaking the law but still get the behaiviour you want) or you don't use the physics engine and script it yourself (as most everyone does for player movement for the reasons you have found out!)
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