I think you are on the right track. I typically will build the knee wall/pony wall as a 3 or 4\" thick section - allows for electrical outlets on the lower working side of the wall. I agree with your proposed technique - using an assembly. One or more cabinets create the island, another cabinet can represent the knee wall. Add the countertops and finish panels and it should sell itself. Good luck.
I have done some very basic ones where the back has a negative top inset of 6\" raising it to 42\". This does not allow for electrical but can be built like a regular cab. If you are interested in this basic design, I can post a picture.
Granted the pony wall definitly looks bulkier and would add to the looks.