Andrew,
As you know there are many, many customization points within PureConnect. Most of these get called as part of general operations.
My understanding is that the difference between "ACD" and "Custom" workgroups is solely to do with initially starting the ACD engine. When you transfer a call to the queue from Attendant, Basic just works (with some configuration limitations) but Custom required modification of CustomIVRWorkkgroupQueue. This allows you to pull such fun stunts as including Desire to Use in the calculation, or setting ranges on Skill proficiencies, or messing around with the various weightings etc. At all other points in the process, as far as I am aware, it's the same.
If you need other Customization Points to only have an effect for your Custom queues, then I suggest setting a call attribute in CusatomIVRWorkgroupQueue and then test for it in the other Handlers, simply return if it's not there (indicating it's "ACD")
Also, I'm curious, "CBR"? That's a new acronym for me.
HTH