Yes, that's pretty much what I had mind with the comment above. Would you like to give it a go? That'd be great!

The problem would be to use addGlobalOption() to update the map

A problem in which way exactly? The calls to MongoDBGlobalContext#replicaSet() would add an option of a new type to the current configuration context (see MongoDBGlobalContextImpl for an example). Then in MongoDBDataStoreProvider the option value could be obtained.

API-wise, I kind of like the fluent approach:

configurable.configureOptionsFor( MongoDB.class ) // returns MongoDBGlobalContext
    .replicaSet()
        .member( "host1" ) // default port
        .member( "host2" )
        .member( "host3", 27018 ); // explicit port