This message was deleted.

Is this for some private plugin or for something public? If it is for a public plugin, it is extremely bad practice to add arbitrary repositories from a plugin. Because there are for example policies like "only use in-house mirrors of repositories". There is even a setting in settings scripts that prevents to declare repositories in build scripts or plugins. Besides that, if you mean with settings repositories, that you declare them in

dependencyResolutionManagement { ... }

then yes, what you see is expected if I understood you correctly. You cannot add repositories in a build script or plugin to the setting script defined ones. You either have the list in the settings script or the list defined in the build script / plugin. Which one is taken if both are present is configured in the settings script, or whether to fail if a project or plugin tries to define some.