I'm not getting a repro on that, @sharkee. Fresh Win10 v2004 VM, not joined, downloaded LGPO, Policy Analyzer, and the Win10 v2004 baseline. Ran the baseline install script with the non-DJ switch. Ran PA, imported the baseline, selected it, compared effective state, and there I filtered out the Server-only GPOs using View | GPO filter. I also selected View | Show only differences. The only settings showing under "Baseline(s)" that varied from "Effective state" were the three settings that get changed for non-DJ: LocalAccountTokenFilterPolicy and the deny logon rights for "Local account."
Make sure there weren't any "path too long" errors when you extracted the files from the baseline zip file and that all the baseline files were present.