Where should the brake calipers grasp the rotor?
Some amount of unworn upper lip on the rotor is normal. For example, when you try to measure a round-edged rotor with a caliper, usually it doesn't work from the outside edge because there's some kind of lip there. The entire brake pad surface should be contacting rotor - in other words, there shouldn't normally be any lip getting worn into the pad. If there were, that would be your real sign that the pad isn't making full contact. But because it can't be totally perfect, it follows that the rotor is wear the unworn spot is going to show up. This one does look a little more extreme than normal, but I think it's fine.
The first thing I would do if I suspected a problem is check firsthand that the mount is actually to spec, since it's pretty simple. Use a caliper or even a pocket rule and poke a skewer through the axle without the QR nut to give you an easy spot to measure the center of the axle. Here are the dimensions. If it's not that then it may be a peculiarity of how this rotor is getting along with this brake and adapter. In my experience, even though it's not supposed to matter, you can save yourself some grief by mismatching adapter/caliper/rotor as little as possible, and you've got a different brand for each here. I do tend to be willing to put in Shimano rotors on anything. (Just to be clear, mismatches shouldn't matter and usually don't.) I think part of what may actually be going on here is the pad type used by the HYRD is just a little taller than most or all of the SRAM/Avid pads and it's making it look like the rotor wear is going further than normal into the large cut-out section of the rotor.
Up to 2-3mm or so should be fine if you want to try this. I would feel like I was doing something wrong if I stacked them up any more than that in a shop setting. I don't really think it's worth messing with upon further consideration.

Edit: Substantively changed this answer after thinking it through a bit more.