Remove dependency on populating top-level document paths

Re: #8273 and #8247, it looks like we sometimes depend on setting `populated()` in the top-level document (https://github.com/Automattic/mongoose/blob/dfde779139a41820ddfb55dc7f088636e80e9f0f/lib/document.js#L1151-L1159) and sometimes we don't (https://github.com/Automattic/mongoose/blob/dfde779139a41820ddfb55dc7f088636e80e9f0f/lib/document.js#L1137-L1139) . The latter is the better approach because once you have populated paths within a document array, or populated paths within a single nested doc within an array, it becomes increasingly difficult to figure out populated values for the subdocument you're looking at.