Docking not that big a problem.
When working on the Alternate Access project, we came up with alternative versions for the APAS androgynous docking system (shown in your picture), the old probe-and-drogue Russian docking system, and even the CBM (Common Berthing Mechanism.) Each has pros and cons, but there is no reason that a properly designed CEV could not accommodate any of them.
In fact, a good designer would make it so that modules for any of the docking systems could be affixed to the CEV, depending on the mission. Wouldn't be that hard.