Chris, the module is not designed to override the query, however you could achieve this by doing the following steps. All javasource, including the replication.jar is readable so you should be able to see the current implementation.
This should be sufficient, however if you do this make sure you take a good look at the alias mapping in the original code replicationsettings code. The generated alias determines how the table and columns are mapped later on in the process.
Just let us know, If you get this to work and you have an suggestion on how to improve the code to make this easier for you so future db replication releases don't break your code.