My guess is the cost differences are still there, but the increases in capicity and decreases in all costs combined with the difficulty of users to control traffic at that level mean that you would really only see this if you're buying a lot of transit. If you're just a residential customer, it might be more likely to impact you as your ISP may have more congestion on oceanic routes rather than an explicit charge.

I do occassionally see hosting operators that will optionally charge more for access to some routes that are better but too costly to include in a bundled rate.

Most of the big operators have peering agreements in place, but that doesn't mean every participant has infinite bandwidth. Google Global Cache and Netflix Open Appliance go a long way to reducing costs by avoiding interconnect where possible.