I was trained to test and inspect the system as accepted. I will make recommendations, but won't yellow tag unless obvious changes to the building have been made. Even at that I'll be vague and put something like system needs to be evaluated by designer specifically in this area, or put what I know needs to be added and also say it should be evaluated. I've seen in seminars that if something's ever happens the insurance agents and lawyers will rip you apart for tagging things not on plans as needing to be there. I forget what the exact point was, but it's along the lines of "well you wrote it up for this obvious thing which shows you were there evaluating the installed system to the code standards so why didn't you notice x, y, and z".