Note that what Apple refers to as the SMC (it's usually known as the EC/embedded controller/keyboard controller in other laptops) is another programmable controller, one that runs as long as the system has power - even from the battery - and is responsible for actually powering up the main CPU, so an exploit could hide itself there too and be even more difficult to detect. The main difference is the SMC/EC has much less memory so what can be hidden there is relatively limited.
Now I wonder if anyone has made a port-80 diagnostic card (dongle?) for Thunderbolt... http://en.wikipedia.org/wiki/POST_card