Why is my Ultegra 6600 much noisier when cross chaining compared to my Deore XT M8000?
I am not sure this is a fair comparison. 6600 ultegra is now three generations old (6700, 6800 and now R8000 come after).

I rode 6600 for many years, rear shifts are still among the fastest out there. But as you noticed cross-chaining was not great. 

I moved to 6800 last year. Shifting speed was compatible (I still feel that a well maintained 6600 is faster, but we are splitting hairs), but cross chaining is much better.

When 6600 came out in early 2000s 11-25 was a monster road cassette for climbing. My current road bike has a 12-32 and I would not go back to a smaller cassette unless I was racing cat 1/2 again.

By comparison XT M8000 became available on bikes just a couple years ago so it represents a much newer group set. A lot has changed in intervening years, and Shimano has tweaked their offerings to match market demand/ current trends.