Saturday (July 26), I fixed the zero clearance function so that now there is a "zero absolute clearances" and "zero relative clearances" option. In previous versions, there was only the relative clearance version of the function.

The difference is that the absolute one sets the clearance to the lowest level in the game regardless of the base height, and the relative version just sets the clearance to object's the base height. If this is confusing (it should be), just use the absolute one ;) .