Figured it out. The MDIO pin and reset definitions are missing in the .dts file which causes the kernel to panic or, with newer builds, to endlessly retry communication with the switch. Once those are fixed the MR9000 also boots OpenWrt from flash. Why it works at all for the MR8300 without those definitions is rather strange since both devices share the same hardware design apart from the 3rd radio.
Getting the 3rd radio to work was straight forward, replacing ath10k-firmware-qca9888-ct with ath10k-firmware-qca9984-ct and extracting the board calibration files from the OEM firmware was all that was needed.
After applying those fixes to NoTengoBattery's build (in a very dirty way I'm sure) I was able to build and flash a working firmware.