Take a Large Stone in your hands.
Press G to initiate the throw wind-up.
Look directly up [0,1,0]
Hold left mouse for max windup time - 5+ seconds?
Release the left mouse.

Please let me know if you are not able to reproduce, happy to provide additional information as required.

Tested on a local server with no mods.
Client and server both 1.21
Never tested on the previous version.
Tested on various surfaces (dirt, road)

I noticed that if you throw off-vertical there is a chance the rock will clip below the ground and bounce up. Makes me feel like you have already implemented a catch for this case and it relates to velocity?

Small stones consistently stop just above the ground and roll, while Large Stone does not have this.

In some throws large stones will bounce off the ground surface and then clip through the ground on the second contact. Or this could also be on a roll of the object.