It doesn't work.
This new arrangement is already in place in my local store (Birmingham, UK). Apple staff are great and I can't praise them highly enough, but the retail experience is appalling. The store is too small, there are people waiting for appointments all over the place, customers and genius bar staff are literally falling over each other on both sides of the genius bar. It's also a security nightmare being squashed in there like sardines - I always feel like I'm about to be pickpocketed.
Then there's the awful experience of simply trying to buy something - I've left on several occasions because I just couldn't get served.
What's needed is a single "Pay Here" location with a good old fashioned queue and people who simply take money - they don't need to be product trained, just till trained - and fast. This would free up time and space. Though I'd go as far as saying that retail and genius bar (or any after-sales service) shouldn't even be on the same floor. If anyone can afford multi-level stores, it's Apple. The stores are too small.
The congestion is 90% genius bar and accessories sales, so those operations should be moved to an area better suited to after-sales - like a different floor.
Did I mention that the stores are too small? ;0)