DeployR - SetupComplete.cmd - LGPO Machine Policies

Migrating over from MDT and I've been trying to apply my local machine policy file with LGPO.exe, but I just cannot get it to stick when using SetupComplete.cmd. AutoAdmin/RunOnce works as expected.

I have migrated my local machine policies to deploy with the PolicyFileEditor PS Module, and that is working, but I would prefer to use LGPO to do it if possible.

I don't believe this is a bug or anything with DeployR, just hoping one of your deployment experts might have some insight.