I'd try to share the config space as much as possible. Options 1 and 3 make sense then.

What feels "right" to me, when using NixOS and its module system, is that all config has the same shape, and is therefor easily moved to a different section, or to a section that is shared by a subset of plugins.

Con: It could lead to bad practices like strengthening dependencies between plugins (if they hard code to use a specific config option of another plugin).

Pro: But if you can discourage that, or use "deprecated pointers" to the new location of an option, the ease of moving shared config options to a more generic level can make it easier to maintain the total configuration. Developers of the separate plugins can build on what others have already done, and even synergize functionality (add a convenient integration if they see another option configured).

If some options are "secret", though, and you don't want those shared, they should either be in their own config (easier), or you'd need some access control on the configuration storage/file for each plugin (more work). Allowing a plugin to have a separate file for credentials, for instance, could be a good choice.