During the performance test, don’t forget that you need to create the actual real time system usage model. (i.e.) The test should be very realistic in such a way that it models the real time traffic & more important is it should model the transaction mix of the real time workload. If you are scheduling a test for 100 users, then make sure that the 100 users are distributed across various functional flows of the application (Say in a banking application during the peak hours the users are distributed across various functionalities like, 60% of the users depositing the amount, 20% of the users transferring the amount, 10% of the users checking for the account balance & 10% of the users accessing the mini-statement). Unless this kind of mixed mode scenario is adopted for the testing, we might not end up simulating the real time user load.
There are certain situations wherein we might need to schedule the performance test with a single functional flow. One situation is when the performance testing is scheduled for each of the functionally stable build. Other situation would be when we identify some performance issues during the mixed mode scenario, then in order to isolate whether the performance issues are from a specific functional flow, we might need to run single functional flow test.
Observe the differences quoted above. As long as your objective is to test the system performance for a specific load, make sure the load is very realistic to the real time user access.