Hi @PhoenixMage,
Not sure I understand the situation correctly, sorry. The BeaglePlay and BeagleBone AI-64 use a very similar booting strategy (U-Boot to GRUB).
There, the enabled MENDER_FEATURES included mender-grub, causing the integration to be injected into GRUB. Do I understand right that this is also the route you are following?
Additionally, it sounds like you have mender-image-uefi enabled and want to use the resulting .uefiimg. So the problem is not having a space reserved for the U-Boot environment? Or what causes the mentioned clobbering of the boot partition?
Greetz,
Josef