I kept forgetting to post an update on mine - sorry.
The 5F unit was replaced under warranty. It was unclear whether this was an attempt to fix the crackling, or just because it threw up a different error message at the garage. The new 5F unit did seem to improve the crackling slightly, but it was still there and very noticeable. By this point i'd given up hoping to get it resolved as the two dealers I took it to admitted they couldn't really hear the problem....
Out of the blue I had a call from my local dealer to inform me there was an MMI update available for the car, which needed me to bring it in. The only release notes for the update stated it was just a generic software update on DVD. After they had done the update I noticed a few things:
1) A whole heap of Bluetooth fixes, I now had the 'Messages' option in the MMI. As well as full support for my Nexus 5 phonebook which previously hadn't worked.
2) Map updates
3) Sound system update
4) General bug fixes / MMI Menu updates
No. 3 provided the most interest. I noticed new options in the sound menu (I can now set focus to rear, instead of just front / all). I also noticed they appear to have changed the EQ settings, and miraculously improved the crackling! Now I can't be sure, but I think they have tweaked the trebble, or reduced the top end on the EQ in order to minimise the crackling. At the same time it feels like there is waaaaay more bass / punch to the system, to the point where I turned the bass down for the first time ever.
This is all very subjective due to the lack of any release notes, but I've had a good month to listen to it all carefully so i'm fairly confident with my analysis. Has it completley removed the crackling? No, but now I think you'd struggle to hear it unless you knew what to listen for, or had heard it before. I'm not sure whether the root cause of this crackle is faulty hardware (to which they've applied a software 'fix'), or a generic software issue. But either way, I suspect cars being produced now will have eiher corrected hardware (5F unit or Amp) or will have this software update applied from the factory.
All my opinion, happy to be proved wrong of course