Not my experience with EBC HH and Gen II FJR rotors.
Don't think there is any magic with the design and specification of rotors or pads although it is logical that a manufacturer would not knowingly use materials in their sintered pads that would damage the rotors that they sell. You have the hardness of the metal "sinter" and the substrate that holds it vs the rotor made out of some specific variety of stainless alloy. I don't know for sure but I suspect very similar (rotor) alloys are used by most manufacturers. (Probably a bit more "black magic" in the design, composition and manufacturing process for the pads.)
Similarly, I would expect that an aftermarket huge company such as EBC would be aware of the applications where people are using their pads. Making especially aggressive pads that caused physical damage would not be a good business model if you are trying to sell to the typical consumer (non-racing) motorcycling public. Who would ever buy them a second time? Not to mention what it would do to the company reputation.
I will say that I haven't personally had issues with the EBC HH product but I am aware that there are some who have had problems. Bad batch of pads? Bad batch of rotors? Who knows? Safer to use Yamaha pads? Maybe and especially if the bike is under warranty. While "wear items" (pads, rotors) are not typically covered, you couldn't even make an argument with your dealer or Yamaha corporate if you used anything other than OEM.
Note: The Yamaha brake caliper and pads are Nissin. Anybody know who makes Yamaha rotors? Very likely that Yamaha produces a design and material specification and jobs it out to the lowest parts bidder - quite possibly the same supplier for many different manufacturers - possibly even EBC or Galfer.