Are you using externalsrc types for the kernel and U-boot? I’m not sure if our logic works with that. You may have to do a completely custom setup. @kacf do you know?
I believe using externalsrc should work, though I have not used it in a while. I do know that when using it, no patches will be applied, neither the prepared ones nor the auto-generated ones. So one has to apply all patches manually in the tree you are building out of.