@klorydryk custom links plugin is not maintained since several years, but can be easily fixed I think.
For the logo and colors we added CSS variable fallbacks, but yes it may require a small adaptation especially if you use raw CSS selectors that are not part of the plugin/theme API.
The new CSS theme system is more easier to override: https://docs.joinpeertube.org/contribute/plugins#css-variables
And we plan in the future to support new menu items by admins in PeerTube core.