A single joint can only cut an opening in a single face. To make a thru mortise, you need to create 2 joints, where each cuts into the opposite face. Just like in the shop - you cut from both sides.

Here's an example:


Here's a closeup, outside of the model:


The tip of the tenon is just simple geometry at the same level as the main timber. The housing and tenon are a standard joint component like always. The piece that's highlighted is the other joint. It's a flat (2D) object that I call a "cutter". CB.