Different Junker groups is a great idea, in my opinion. It really fits in with the overall feel, I've what I think, the Junkers are all about. Separate states that will join when needed for a singular cause.
I will have to agree that the 'Independence' part of the title can be confusing. Though I get the idea. I would suggest moving toward changing it. Maybe something like, Junker Rights Movement. If only to alleviate confusion.
As for the pirating. Junkers are opportunist. (Generally speaking.) They'll take what they can get, when they can get away, scott free. In order to keep their quasi-legal status, brazen piracy might not be a good idea.
Certainly not in the house systems. So I would suggest only pirating in border and outer world territories. Legal entities are not really going to see .:j:. or JRM. They'll see Junkers. However, I would like to see more piracy for actual loot, not cash. I think the Junkers could fit that bill. Specific technologies not available to certain clients. Since Junkers are know for their technological craftiness, I think this could work well. And maybe could tie in with the parts supplying to Gallia.