This may well be the case, what they were implying is that it is ok to modify it but if your warranty claim is directly related to the modification being the cause then they will look into it harder and not warrant the vehicle. They said that they can see exactly what happened to the vehicle via the computer so if you have a tune then reflash it back they can tell exactly when that the tune was done and removed so one is assuming that if the problem occured during the "tuned" period they may not want to honour the warranty. That is why I was told there is no point in hidding the mods as they know anyway. Changing the exhaust is no issue, they even mentioned Willall as being the best. How is that for advertising. So based on the advise I will probably only change the exhaust which I think is about all I would want out of the car anyway.
I think the main and most interesting point I was making is that they will work on JDM cars which I actually found to be impressive service given everything else that has been flying around.