You can clone with
Model::all() currently adds rev and id keys with null values to resulting collection of docs. Imagine CouchDB::_format() is being applied to results. Couldn't find applicable unit tests but perhaps this is more an integration test anyhow.
It may have been solved in the last dev. see 5523739
Wasn't able to reproduce your issue with the last dev. Feel free to reopen it with a small example if this still an issue. ;-)