DBClientBase constructs commands using the logic meant to upconvert legacy OP_QUERY commands rather than just producing OP_MSG encoded messages directly. We should update it to stop doing this so we can delete some of this legacy code.

https://github.com/10gen/mongo/blob/a5f44838e110d0da7b9ceaa083b343f8b43b08f3/src/mongo/client/dbclient_base.cpp#L264-L269

As part of this, we may need to change the mongo runCommand helpers, as they currently use flags like SecondaryOK for specifying secondary read preferences.