Those machines really are for prototyping and small batches only. They work in a sequential manner, so every pad you add increases your production time. You don't want to wait for a board with a few thousand pads! But a good stencil costs way more than the time you put into this.
Misalignment is also a very common problem in solder paste printing, you have production offsets in every component (okay, here you only have a PCB...), further it's very important to choose reliable fiducials. After all, some fine tuning to eliminate the last offset usually doesn't hurt! But for a quick demo the result isn't bad at all.
Here at work (German University, research in electronics production) i'm sitting next to the exact same machine - the Martin Dot-Liner-06 - every day! Just haven't used it yet, i think after your video i might fire it up some day