You are correct, there is no way in the object model to set the FEM units. You can create the project in HyperSizer, go to the Import/Export options and change the import units, save the project, and then go back to the object model to continue on. Version 5.3 also gives you the ability to right click on the units in the Import/Export form and save any unit as a default for this database. If you do that, then every project created from this point forward will use your chosen units.
Note, there is a difference between the FEM Model units and the Project Units. The FEM model units are used just to know how to import the model and export the resulting stiffnesses. These settings will not affect what you see on the sizing form. The display units are all governed by the project units. This means you could have a model in SI units, import it, and do all analysis and sizing in English units, and it would put out the stiffnesses to the FEM back in SI units.