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Debian/Ubuntu

• /usr/share/ca-certificates is reserved for files managed by package managers
• user customization should be placed in /usr/local/share/ca-certificates
• mention that CA certificate must have .crt extension
• /sbin/update-ca-certificates is easier to remember than dpkg reconfigure

Fedora/CentOS/RHEL

• place certificate in /etc/pki/ca-trust/source/anchors/
• run update-ca-trust

After studying your Emacs configuration (Nederlanders zie je hier niet zo vaak trouwens), what about using https://github.com/jwiegley/use-package to group your package configurations, and group them into different files in one directory, and lazyloading them (only load the files when needed) in your autoloader.
For example config-magit.el with your magit settings and keybindings in use-package declaration, with the following sentence (provide 'config-magit) included:

Then

 (require config-foobar
              config-magit)

In your init.el