Can you use Universal IO instead? I've been working on a PRU project and found it saved me a lot of trouble tweaking the Device Tree.
I started using this rather than editing the Device Tree, and found it managed the PRU pins adequately.
So I had the intention of returning to this problem and building a custom DT.
The Beaglebones have plenty of resources to handle this, so why not use it permanently?
Perhaps if you are using a cape type plug-in with stored configuration a custom DT would be mandatory.
Note that you can put all of your pin configurations in a text file and load them with the config-pin -f option.
Put this in whatever start-up configuration you use and you are good to go.
Greg