How do I change the success message background color on system pages?

That background color is coming from Theme editor (Global theme styles) > Global colors > Tertiary color.

If you don't want to change it from your theme editor, then you can use the custom CSS below:

<style>
  .systems-page .success { background-color: #E5E5E5; }
</style>

Play with the color value as you wish.

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