The most robust method is to not use themes. Instead, disable the installation of the Aero theme, which then puts Windows into "Custom" theme mode, allowing a user to modify settings however they want and without them being overwritten anymore. I have explained these details in many posts, which can be found by searching the forum (
link1,
link2). A user is then free to modify cosmetic settings in NTLite or through the integration of registry files into an image, without interference from the Aero theme.
There are many settings that can be customized, and it is not practical to list them all, instead it is more efficient to download a registry compare tool, such as RegistryChangesView by NirSoft, and then toggle options through the Windows Settings page and Control Panel, while taking snapshots to obtain the registry keys needed, for integrating into an image. I already have hundreds of customizations available in a downloadable registry file from this guide (
link3), which can be used as-is, modified, or just serve as a learning example.
The registry method is superior to all others, since it addresses the root of the problem and produces no quirks or bugs, making it so that theme customizations apply to all users out of the box, while still maintaining the integrity of the operating system.