All very interesting comments but what I think we need to differentiate between is 'Test Flying' and 'Mission Equipment Evaluation'.
Early stages of 'Test Flying' (Experimental) for example or New Build can be very risky. I normally work to obtain a C of A first. During this process 'Role / Mission Systems' could not be further from my mind. Principal Flight Airworthiness is tested and confidence in the machine slowly built up. This is fundamentally because your personal safety is threatened at that time. Once a C of A has been obtained then 'Mission Equipment' tests can be considered. Airworthiness tests mainly around flight dynamics are carried out first and airworthiness established for the 'Mission Equipment' modifications. Up until this point TP & FTE only are used. Sometimes (But very rarely) a third crew member may be involved e.g. Airworthiness Authority Surveyor. After this 'Mission Equipment Operational Evaluation' is normally Low Risk and of a none airworthiness nature. In my experience I have generally found that rear seat equipment operators are not required for small civil aircraft. However, Large Military or Fast jet Mission equipment can sometimes be evaluated by specialist equipment operators trained in military operations evaluation. I must highlight though that at this point this is no longer by definition a 'Test Flight'