How can I get a setting from a particular entity?

The suggested MR adds support for retrieving individual instances of settings with the instance ID. It should be backwards compatible with the tokens that were there before.

Adjusted issue summary and subject.

Every setting (bundle) has always 1 and only 1 associated entity. That's something we're not going to change. If you need multiple instances of the same bundle, I recommend you use the Site Settings and Labels module → or you create a setting with a multiple entity reference field referencing another bundle, using the Inline Entity Form widget → .

ah ok that's unfortunate. The module lets me add more than one instance of each setting so I thought this may have just been a usecase that wasn't considered.

The module doesn't let you manually create settings entities, it creates 1 entity automatically. You might still be able to manually create entities with user 1 since that user bypasses all access checks, but there isn't much we can do about that.