For certain I see two problems.
1. He is using precise fitting mortises and claims a perfect fit. What I consider a perfect fit and what he may may consider a perfect bit are apparently not the same.
If you go to precisely 5:41 on the video and see him using a rubber mallet to close the joint look closely at the left upper stile. The end of the stile protrudes past the edge of the rail. There is no way to fix that short of cutting the ends of the assembly after glue up. I use a precise fit mortise on one piece and an elongated mortise on the mating piece so that I can tweak the fit to be perfect.
2. He uses the bottom of the Domino mortiser as the reference. This can introduce all kinds of errors. The best method is to always use the fence as your reference surface.
Using the bottom of the Domino will cause misplaced mortises if any of the following conditions exist. And who has never had any of these conditions?
A. The work surface or the work is not perfectly flat. If the work and the bottom of the mortiser are not on the same plane the mortise will either be too high, too low, or at an angle. If the work has a slight bow the mortiser will cut into the surface of the work at an angle, not a perfect 90 degree angle.
B. Debris under the work piece or the mortiser can throw alignment off. Is there saw dust in your shop?
When you use the fence, you can see the top of the work and if it has any dust on it. You cannot if the debris is under the work. The flat fence on top of the work always registers the tool to the work not the work surface. On thin pieces of wood hang the edge or end past the end of the work surface so that the mortiser does not register against the work surface. Even on longer bowed boards if the fence can rest flat on the end or edge most of the bow is taken out of the equation.