I'm the maintainer of the meteor-sharejs package.
The recommended way to use the package is to keep all metadata in a Meteor Collection, and not in the ShareJS docs collection. This is because they are basically separate software stacks that do not talk to each other. It's also possible that you are using a docs
collection for your documents which is the same name as the ShareJS collection; then they would be overwriting each other.
If you'd like to see ShareJS not head in the direction of being compatible only with Derby, I'd encourage you to chip in at https://github.com/share/ShareJS/issues/277.