Few questions on having and engine built.

If I am having them assemble the entire engine then I will want them to set the timing and tune the carb. so it is running great.
I am not trying to be mean in any way but this sounds like a too-generalized way of looking at things that will lead to troubles. The last phrase is the problem...... define 'running great'. That is what you need to speak with them and think about and mutually come up with some objective measures of performance that they can work to on a dyno, not some subjective criteria that you can interpret differently than them.

With a dyno, they can't spend the time in the car that will really load the engine and run it at all sorts of different environmental situations as it will really see on the street. Dyno loading can only find so much. So if they run it to peak HP or something like that, it may still have things like slight off-idle flat spots, poor fuel economy, etc.

I build systems (non-automotive) all the time for a living, and we always put down objective criteria to meet. When folks start becoming subjective ("it's slow") then I have to get technical and ask "So exactly how slow is it?"