rs.reconfig() blindly updates the version to the current version + 1. This makes sense if the user doesn't specify a version already, however if the user is providing the version it should be respected. This can lead to race conditions where two or more users update and overwrite each others changes.

I've verified that replSetReconfig command does the right thing (both anecdotaly and in code https://github.com/mongodb/mongo/blob/master/db/repl/rs_config.cpp#L244-248).