I would say that if the same OEM pistons are used when they rebuild the caliper, than it is likely that the same problem will develop. Thought it was worth a try to see if Triumph can figure out the problem and fix it, but if they don't I'll just do it myself.
From talking with the service manager I get the impression that they're sort of taking the shotgun approach with the issue - change everything and hope something fixes the issue, rather than really finding the root cause and addressing it. I really tried to impress on him the issue with the aluminum pistons when I dropped it off, but I think that Triumph is calling all the shots on this one, not the dealer. So if they're replacing parts they're probably using Triumph OEM, and unless Brembo has made a design change in the caliper or pistons they are supplying, I'm likely going to get the same pistons it originally came with. Likely that they'll replace everything, put new pads in, ride it 50 miles and say that it's working just fine. Then I'll ride it 1000 miles, wear in the pads, and have the same issue all over again.
Not sure that the troubleshooting methodology is working very well on this one from Triumph's end. That said, I'd like to thank all the folks on this board to did a great job troubleshooting and finding the true cause of the braking problem. Well done!