Hello there,
Thanks for the status update. Good to hear that you got this working.
I believe this might help you with your issue here: Preload Device Tree Overlays?
On this post, my teammate explains how you could bake in the custom dtbo into the image before flashing your RPi. Have you tried that already?
On other news, one of my balena teammates recently gave a presentation to the team on improving this workflow to load kernel modules. Not sure when we will release that feature but it will get easier to load kernel modules.
Cheers…