I would suggest you firstly make sure the stability of your sdcard when you boot from emmc. Actually, your device tree change lacks of some properties.
For example, our developer guide mentions there is cd-gpios and SDMMC_VDD_EN. But they don’t show up in your device tree at all.
I guess your sdcard is not even working when you boot from emmc.
The system currently work when i start with the emmc and is possible to mount the sdcard without problem and copy the root.
I can boot from the sd card modifying the extlinux.conf without problem.
The problem appears only when using the sdcard mounted as / and booting normally if i need reboot using a software command like: shutdown -r now appears the panic screen.
But if i made a cold reset then system boot without problem.
And based on our experience of helping bring up extra sd slot on production modules over TX2-NX, NX and Nano, cd-gpios and vmmc-suppply in device tree are needed.
Sometimes user may think their sdcard is working but it may not be true. Because it has chance sdcard is enumerated in low speed mode due to those properties in device tree are not correct. Under such case, yes the sdcard is working, but it is not right.
Generally, we ask for schematic (sd part), full dts file and dmesg to debug.
Please do not modify tegra210-porg-plugin-manager.dtsi. You should not touch this if you don’t understand what this is doing. Just prevent to use those plugin-manager stuff. This is usually doing board dts control for our internal board.
Also, please use dtc tool to directly convert your dtb back to dts and share it here. It looks like your vmmc-supply is not correct.
BTW, generally we ask customer to assign vdd-3v3-sd, which is regulator@3 to the vmmc-supply. But in your device tree, you give regulator@2, which is vdd-3v3-sys to vmmc-supply.