I have the same issue in my application.
When applying feature usage reporting to the different assemblies, this results in each assembly being considered a different "version", even if the have the same application name. So even if they belong to the same application, you will see the feature reports being split up. Depending on how you handle asking the user for consent, this can also result in a prompt for each assembly.
The way I solved it was by having a method to report usage in an assembly known by all assemblies, which is wrapper over the actual call to usage reporting. That way, there is only one assembly which gets feature reporting compiled into it, and thus all feature reports for the application appear together.