Editing theme files and access to the Code pages only to super-admin?

If that is custom functionality in theme options page then it is highly specific to that theme. Likely you will need to edit theme files and/or create child theme. Plus option pages can be simply in WordPress API but just as well can be built with help of theme framework or other kind of third party code.

I think your first stop should be developers of themes and information on how to best work with their option pages.

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