I don't understand why you would need to profile these apps any differently. You want to profile how your app behaves on the production server - go ahead and do it.
A single request will still be executed on a single instance, and you'll get the data from that same instance. If you want to profile services located on a different physical tier as well, that would require different approaches; involving communication through internal endpoints which I'm sure the mini profiler doesn't support out of the box. However, the modification shouldn't be that complicated.
However, would you want to profile physically separated tiers, I would go about it in a different way. Specifically, profile each tier independantly. Because that's how I would go about optimizing it. If you wrap the call to your other tier in a profiler statement, you can see where the problem lies and still be able to solve it.