Hi Tom,
Your stock ECU will cope with changes to the exhausts and air filter. It's only when you go to higher lift cams, such as the 569, that the ECU needs re-mapping. .
For info, I doubt very much that MMC would reflash an ECU for a third party upgrade as the reason it is locked is to meet emissions regulations.
When the Stage 2 cams are used you will get the message on ProTune , “exceeds maximum limits” or something to that effect but it does not say which limits it exceeds. Do you know what has been exceeded?
It's the Fuel Trims that reach their limit. There's probably 10-15% flexibility in fueling control within the stovk map, in response to the Lambda sensor output. Stage-1 allows a better flow, resulting in more air and more fuel requirements. There's plenty of headroom available in the injectors (known as their Duty Cycle) and indeed stock injectors are fine with Stage-2, 569 cams, but the stock ECU map can only compensate by a cerain amount. When the lambda signal says I need more fuel, but the stock map says that it's giving all it's allowed to do, then a Limits Excdeeded message gets flagged. Risk is that the engine will be running lean, which isn't great, but in truth it's unlikey to be that far out with just a Stage-1.