I had PPE Downpipes on my Ford Flex as well as a 3 bar sensor, 10gpm methanol spray nozzle and a Torrie tune.
I did not have any drivability issues nor did I get codes from downpipes for the first 30K I had them on. Once they coded Torrie just turned off the code in the tune.
Any flashing of your ECM will void your warranty if you still have one. When I had my engine issue ( totally my fault), Ford told me that even though tune was now stock, that I had flashed the ECM over 100 times and the last flash point was 12 miles before I took it in. This was on a 2010, so the newer the vehicle, the more information they likely can pull out of the ECM.
Once my engine issue was resolved, I drove the Flex for another 75,000 mi with a mild tune and no mechanical issues except for some whine in my transfer case that the dealer found, but I hadn't noticed. This happened at around 93K. Considering how hard I drove the AWD system in the first 35K, my Flex definitely OVER achieved.