I imagine that what they do is a lot like what these peolpe do:
http://www.motec.com/home.htm
I worked on a XKE 12cyl that had a HE system (Jag) but with everything but the injectors replaced with the Motec system.
I had to do some diagnostics and they sent me a program for my laptop. I spent some time and came up with the conclusion I might have a bad controller (isn't it always the way). When I called the guy he said it was very unlikely that it was the controller and he helped me a lot, but he also told me the control unit I had cost over $10,000. Go to the site and you can see some of the cars that run these systems.
Theyare basically plug and play. They have some mapped values and can use many types of inputs. They are also designed to be tuned by a race program. Everything is adjustable. Believe me you don't want everything adjustable unless you have a dyno and a lot of time