I can second the TRP Spyre brand of brakes.

I have TRP Spyre-C twin piston on my Fuji and don't even notice they're there. I've been a disc hater since the day I got discs on my old Crossrip around 2014 (avid bb7's)...when I picked this Fuji, I specificially picked something that had good reviews on upgraded discs...and I'm happy with them. I wanted to hate them, so I went into it with preconceived notion too.

Just out of curiosity, have you loosened the mounting bolts, squeezed the brake lever, and then re-tightened them with the brake lever still squeezed? I used to have to center my bb7's like every week or so...and that kept them quiet for a while each time.