I'm dealing with this as well.
I followed this guide written for Mavericks to El Capitan, but performed on macOS Sierra:
https://sites.sas.upenn.edu/jasonrw/blog/2013/03/create-custom-default-user-prof ile-os-x-107108
These instructions worked flawlessly in Mavericks, but I'm also having a few quirks in Sierra.
In my set up, I open some preinstalled programs, like LibreOffice and Firefox, add some bookmarks and install some extensions. I also add those programs to the dock.
I got everything to work, except the Downloads folder in the dock shows the folder icon with the little red circle, as if the user doesn't have rights to it, yet I can add/remove files no problem. On different machines it could also show a giant question mark. Re-adding the folder to the dock fixes it, but that's not desirable in the field!
The few things I did differently were running the Mac version of CCleaner with everything checked excluding 'Custom Files and Folders'. Further down in the instructions, when signed into the 'root' user, I delete the Keychain folder contents then instead of while logged in as the default profile user.
I also found this post: Re: Custom Profile Issue
Maybe that would help.