Dyno tuning comes in a few flavors...
You can use steady state dynos to get the basic mapping for all sorts of engine parameters sorted out, but to get closer to the "real world" tuning you would need tun ethe transients on a more sophisticated (more money) dyno. That is the main reason that there will always be some sort of tuning based on road feel. The transients of driving on real roads and all the variations that you come up against are hard to pre-program for transient dyno runs.
Eddy-current dyno can adjust the load on the engine very quickly and are used to tune the transisents with great succes. They can also hold constant load like the majority of dynos out there (steady-state), so that particular points in the mapping/tables can be adjusted for optimum.
Having dealt with both chassis and engine dynos in the past, I would say that no matter how much time is spent on the dyno, you will always have some tuning to do once the driver gets in the car. The driver can pick up on things that dont' 'FEEL' right better than trying to sort it out by looking at data.
Steve-o