Not at all surprising. Auto manufacturers have been doing this for awhile now. You really can't blame them. If you're worried about your warranty, don't modify the bike. I modified my R3T as well as my car within months of purchase and I assumed the risk in both cases.
I don't know about the Triumph ECU but I do know that a Volkswagen ECU has a counter which shows how many times the ECU has been flashed. So unless the dealer has documented an update, even if you flash back to stock you're still likely to be caught if the counter is greater than one.
That's not to excuse Triumph for denying any valid warranty claims. For what its worth, I've had warranty claims honored for both bikes and cars where I freely admitted to the dealer that the vehicle had been modified. In the US, there has to be a relationship between the modification and the failure in order for a dealer to deny coverage. Now, that's the legal side. That doesn't mean a dealer won't deny coverage knowing not many people have the will or the resources to pursue a claim in court.