You can go ahead and generate the code yourself.
I'm not sure why the generated code would be different. However we do have some discrepancies between the code generated within Eclipse and the one using the standalone generator, which is the one invoked during the build. These discrepancies seem to be about the order in which certain elements (e.g. member functions) are generated (I'm not sure why yet).
Because of these discrepancies, I would suggest to use the standalone generator. The generator is called 'umlrtgen.sh' and is located under 'org.eclipse.papyrusrt.codegen.standalone'. If you prefer to setup a run/debug configuration in Eclipse, here's some guidance:
The run configuration arguments I use for generating ComputerSystem are:
-d -l ALL -s -p /Users/epp/Development/PapyrusRT/ides/mars-sdk/Eclipse.app/Contents/Eclipse/plugins:/Users/epp/Development/PapyrusRT/git/org.eclipse.papyrus-rt/plugins/umlrt -o /Users/epp/Development/PapyrusRT/gen/ComputerSystem /Users/epp/Development/PapyrusRT/git/org.eclipse.papyrus-rt/models/samples/ComputerSystem/ComputerSystem.uml
The model is in the models/samples folder.
Other models that might have the same issue are PingPong and PingPong-data in models/tests.
If you need help with the generation, let me know.