Is something missing between steps 2 and 3?

Maybe nothing's missing.
Recipe says in step 3 cook another half hour or until beans are done.
So looks like the beans are cooking minimum one hour or until done (dried beans - depending on and and type - can take 3/4 to 3 hours to cook).
And all the while absorbing other good flavors.

I think you are right, and there should be a direction at the end of Step 2 to soak the beans overnight (or up to 12 hours). Step 3 involves cooking the beans only for 30 minutes, so there has to be some soaking involved. If adding baking soda were the magic answer for skipping an overnight soak, then every bean recipe would contain that direction.