Just a thought (and I might be barking up the wrong tree here), but Shimano have some issues with higher end road cranks where the hollowtech is in several parts bonded together. Pretty sure I’ve seen pictures of a number of split / failing Ultegra cranks. Are XTR built that same way and something like that could be happening?
Otherwise there’s no real reason I can think of for a ht2 crank to just start creaking over a few years as long as it’s all greased right / bearings are good / it’s all torqued up correctly