Maybe I'm just reading this wrong, but even if the pads start out thinner than before, why would that make people change them prematurely? When you measure pad thickness to determine when to change them, you measure how much friction material is remaining, not how much you wore off from the starting thickness. BTW, the minimum thickness of the friction material is specified as .040" from the backing plate by H-D ( I prefer .060" or 1/16"). If someone decides to change them at .125", that's his decision but I don't think anyone can blame the pad manufacturer for that.
If the complaint is that the thinner friction material reduces the life of the pads and thus increases the owner's cost per mile for brake repairs, that might be true assuming the new pads wear at the same rate as the old pads. It would be interesting to hear from H-D if there was an intentional change to the pad thickness, and if there was a change to the compound. Of course, it would also be interesting to know if those pads the service guy showed you are really genuine Brembo pads. The way things have been going with H-D, they might be a Chinese knock-off.
Here's how you fix the problem. Buy yourself 3 sets of Lyndall Z+ pads, one for each caliper. Problem solved.
Jerry