Thank you for this detailed problem description. I have forwarded it on to our engineering team.
I experienced a similar fan noise, clearly a mechanical fouling sound, with a new D54250WYK. The fix above put me on the right track, lessened the noise but didn't quite resolve it in my instance. I ended up needing to file down the fan blades by about 1mm as shown;
Thought it would be useful to share.
Also this video was also useful to see how to remove the motherboard - Intel NUC D54250WYK - Motherboard and cooler removal - YouTube
Thanks for the information KirkDrage.