Thanks,
The mender-convert you are currently running is using a Mender integration which is based on U-Boot loading a GRUB EFI, which then further boot the Linux kernel. In this case the overlays are indeed ignored as the GRUB bootloader will load the “stock” dtb file. This is just how this particular integration works, and you would probably need to merge dtb files ahead of the running mender-convert to enable what your overlays did.
Though, we have a new release of mender-convert where it will work slightly different and in this case the BBB integration is utilizing a standalone U-Boot integration, meaning that overlays should work similarly to how they are applied in a “stock” image.
I would recommend you to test this out, you can find the new version of mender-convert here (master branch),