Interesting following your issue here, Dallant. I have the same HD-M745 4-piston brakes on my Santa Cruz Nomad with a BBSHD. I already had 203mm rotors on the bike for a long time and had a store of rotors in the parts bin, so I didn't buy the Tektro rotors. The front rotor is an old Hayes that sat in its original plastic for years, while the rear is a low use Avid rotor. The Hayes is 1.9mm thick as well as the Avid. I had noticed the HD-M745 rotors were 1.8mm while the HD-M750 rotors were 2.3mm. Both HD-M745 and HD-M750 brake sets are 4-piston...use the same master cylinders, same pads (equal Shimano fit), but use slightly different calipers. Neither brake set is actually more powerful, but it is interesting that Tektro fitted the 2.3mm rotor with the HD-M750's.
Now, all that said, the HD-M745's are excellent brakes. There must be something in the rotor design from Tektro, however, that is requiring a thicker rotor for these powerful 4-piston brakes. I say that because my HD-M745's are running fine on the old Hayes and Avid rotors...no squealing on braking, no drag off the brakes, and no sound while rotating freely. It must come down to the rotor material, the design of the rotor spokes/holes, or something else. I work at a bike shop, and I've seen mismatched brand rotor and brake sets over years without issue. I've never really concerned myself with having the exact brand rotor to the same brand caliper...as long as hardware and rotor size was appropriate.
Barring a warped or tweaked rotor, your situation reminded me of some instances where pressure in the hydraulic system caused a very slight rub between rotor and pads. This could be from not performing a vacuum pull on the syringes as recommended by some brands and models, or someone not insuring the caliper pistons were fully retracted during service or assembly when new. Regardless it is evident that Tektro makes a thicker rotor for their 4-piston setups, and that probably indicates something in their design. I'm glad they worked it out for you and under warranty. Trek is usually pretty good about that. The shop I work at primarily sells Trek and Specialized.