Are you able to stop in u-boot cmdline and check with
ls mmc 1:2 boot/
ls mmc 1:2 boot/overlays/
if the overlays you need are there, or at least which ones are present? I recall checking CAN overlays on 2.56.0 and 2.58 and they were loading properly, wonder if your additional yocto layer could have anything to do with this.