The package structure in the UML meta-model does not affect any of the generated outputs. The hierarchy of the meta-model is effectively "flattened" during the build process.
The one area where the structure of the hierarchy is significant is that options, which can be specified at package level, will apply to all classes and other packages within that package. However, any option can be overridden in any of the sub-packages by setting the option at that level to its new value.