Greetings @seasoned_geek,
Let’s see if we can clear this up. First of all, are you making U-Boot changes just to change the U-Boot environment variables so that system boots with the Dahlia device tree by default? Or are their other changes you wish to make?
If it’s just the change for the device tree. You should be able to make this with TorizonCore Builder. See this section here: Device Tree Overlays on Torizon | Toradex Developer Center
Basically you can use the dt apply command to set any device tree (even custom made ones) as the default.
Best Regards,
Jeremias