Mythran : you'll need to set my.polygon = on,
and maybe be play with enable_polycollision (Im not sure),
AND in "player_action", in "player.wdl" find the line my.z_offset = something; and set it to Zero.

That should remove the "space" below the model, but I honestly dont know what it will do to the collisions.

I wouldnt be surprised if you get fired into the sky like a rocket at startup.
Make sure your model is positioned just above the ground at level-load or ent_create time.