How to override "active configuration" when the theme is installing?
You cannot. You can provide only configuration for your module or create new configuration entities. You can "override" the default configuration only by profile, not module or theme.

But you can use hook_install to programmatically override whatever you want.

When it comes to themes, the only configuration that you should provide is block instances and your theme's settings. Of course if you have some advanced blocks you can also provide block types and field storage and instances for them.