Mike,
I understand and think it's a good idea to run your engine on a dyno and get the tune almost perfect, before putting it in the car.
Dave did exactly that with my engine. In fact, he put it on the dyno with the alternator mounted, so he could power the ECU, ignition and injectors, etc. exactly as they would be in the car. Fuel was provided by my electric fuel pump, also powered by the alternator. Later in the process he mounted the entire exhaust system, so he could make sure the calibration was OK with the added exhaust restriction. By the time the engine went into the car, the tune was about 99% perfect and we knew that every component was working properly. That only left some final tweaking once the engine was in the car.
It goes without saying, doing a full tune from scratch, in the car, with a very powerful engine, is difficult at best. Especially if you want a great tune at high RPM's. Also, if there's a problem with a component, it's easy to diagnose and rectify, when the engine's on the dyno.
Dave