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From looking at the marks on the rotor where the pads have hit it, they do seem to be perhaps just low enough to be causing trouble with the rotor arms.
Chuck some small washers between the post mount - will push the caliper higher and take the pads further from the arms. See if that solves the issue. If it does, new post mount adapter time I'd imagine, assuming your surly fork is IS.
It's important to bed disc brake pads in properly. It's basically some heavy consistent braking repeated ten or so times with the aim of heating the pad and getting it to transfer material to the rotor. If you don't do this, your brakes won't feel bitey and they'll transfer uneven layers of material on to the rotor causing judder and noise.
Cheers. I mentioned copper grease as a lot of people online seem to have found this to help with their TRP brake judder. Obvs would be careful not to get any on the front of the pads.
This has happened from brand new so if the rotor was bent it came out of the box that way. From looking at the marks on the rotor where the pads have hit it, they do seem to be perhaps just low enough to be causing trouble with the rotor arms. Perhaps. The rotor itself is also grooved, which doesn't look sensible but surely can't be designed so badly that this would be a problem. I'm talking about the black notches here:
Hy Rds seem to have been sold with about 4 very different designs of rotor, from a look through Google images. Wonder if that's significant.
Headset seems free of play, bike shop agreed.