it seems the file that you need to create / edit to enable capes is /mnt/boot/resinOS_uEnv.txt
I just tried this on a beaglebone green with balena-os following this forum thread Beaglebone cape support and it appears to work.
The difference to the above thread is that it is not /mnt/boot/uEnv.txt but /mnt/boot/resinOS_uEnv.txt which is being processed on boot.
Cheers Thomas