Theme dev here: Plugins are optimized to work with default discord alone, and it's the theme developer's fault if theres conflicts. I suggest contacting the creator of your theme for them to add support.
Yeah. We have some pre-made palettes at the slate website. If you want to try and make your own, you can mess around with the code from the site above, and view documentation here.
If you are having performance issues with Midnight, enable reduced motion mode. It disables un-needed animations and removes some extra effects.