Gee, I'm late but was cutBlind what you were looking for?
https://cadquery.readthedocs.io/en/latest/classreference.html#cadquery.Workplane.cutBlind
Basically just draw a circle with the pocket radius followed by cutBlind.
Alternatively (and probably faster!) is to first extrude the cylinder to the bottom of the pocket, then draw two more circles (outer radius and pocket radius, forming a ring) and extrude that to the top height.