I recently ran into an issue with torque, external schemas, and the implementation of the complexDataModel flag.
To illustrate, I have created this github project. As you will see, there are two schema files: first-schema.xml and second-schema.xml which includes the first. The generated base classes for tbl1 and tbl3 differ in that BaseTbl3 has the getter methods for the link table tbl_link_int (e.g. getTblLinkInts()), whereas BaseTbl1 does not.
I think it would be a very useful feature to be able to split a large schema into several sub-schema files and not lose the ability to generate these setters!