Right, final post on my issue - have not necessarily got to the bottom of everything, but I've got as much as I'm going to get, I think.
Have been in discussion with BMW UK's aftersales manager for the past week. Also had some interesting news from the dealership aftersales manager. Dealership aftersales contact claims that BMW had taken the part away and then stated it wasn't something from the factory, so were not going to pay out on the warranty claim. This, supposedly resulted in the job taking much longer as they were doing it in spare time between paying jobs, as I understand. From what I've learned from the UK aftersales manager, this was a miscommunication somewhere, or a delay in actually passing the clearance to rebuild.
BMW UK have now told me exactly what it was (with no real prompting) - a tool used in rotating the engine on the bench when building, which could have fractured in use, dropped into the sump and not caught. Also, non-ferrous, so only came out with oil flow, not the magnet on the sump plug, hence not dropping out on the first or second service.
The aftersales manager from BMW has smoothed it over as best he can - basically apologising for the wait and blaming a perfect storm of factors, including parts delays, delays in passing the work at a head office level and miscommunication throughout the levels. Promises that this has raised several points to address and will change for the future.
The important thing now - the bike is back and in fine fettle (dropped off in a van at my house on Friday of last week). Took them long enough, but the job looks to be excellent - gearshift quality could even said to be a bit better.
Also - from looking at the technical manual - the sump in that engine is actually very contained and pretty tall. Big ends and gear cluster are very out of the way and pretty shrouded. Plus the chunks have supposedly been inspected for crush or impact damage and the gear cluster very closely inspected, also. My concerns about the parts actually rattling about are now pretty low.
On top of this - BMW UK have extended a 2 year warranty on the engine and gearbox as a result of the repair. Can't honestly say much fairer than that...
Am I delighted at what has gone down over the past two and a half months? No. Am I now happy it's resolved for me? I think so. Not without having to go to the aftersales manager for BMW Motorrad UK, myself, though, which is properly disappointing.