Dear @flatz,
I just rechecked it and no, you didn’t miss anything. NAND Modules such as the Colibri iMX7D 512Mb work with device trees a bit differently from other eMMC based-modules. They use ubiupdatevol to update the module instead of the fdt variables in u-boot Updating NAND-based modules from userspace | Toradex Developer Center. Therefore, if your interfaces are there like you designed it’s loading your correct device tree and you should be fine. You can also have a look at this post to learn more: How to copy multiple DTB files via U-boot - #2 by alex.tx.
To be 100% sure that your device tree is being used you could change the following line on your colibri-imx7-my-eval-v3.dts to something like model = "Toradex My Colibri iMX7D and then you could check with: dmesg | grep Machine.
Best regards,