Firstly, unlike color-themes, Custom Themes work
well with Custom. Secondly, they can not only be disabled (minor
modes can too), but, unlike with global minor modes, the user can
safely override the values they set with other themes or through
Custom (but not using setq).
This was indeed the reason why I decided to install Custom Themes.
We will make them work, before the next release.
It just needs doing work.
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