This is a good question! Challenge layers (as dangerous domains are called in the game files) do improve the odds of getting rare affixes (except in “easy” challenge layers).
The tables @mad_lee showed above assume no challenge layer. The relative frequency of affixes within the same tier does not change depending on challenge layer, only the chance of rare vs. magic.
For example, here are the affix combo rates on Ultimate for a Gargoyle Girdle dropped from a Hero mob (or BossChest, in SR), assuming different challenge layers:
No challenge layer
magic/magic 13.31%
magic/rare 43.17%
rare/magic 43.17%
rare/rare 0.36%
Easy dangerous domain
magic/magic 14.87%
magic/rare 42.21%
rare/magic 42.21%
rare/rare 0.70%
Hard dangerous domain
magic/magic 9.25%
magic/rare 45.00%
rare/magic 45.00%
rare/rare 0.75%
Roguelike dungeon
magic/magic 4.66%
magic/rare 47.27%
rare/magic 47.27%
rare/rare 0.79%
Boss chest in SR
magic/magic 2.48%
magic/rare 48.35%
rare/magic 48.35%
rare/rare 0.81%
Edit: the numbers above were for patch 1.2.0.x, for patch 1.2.1 see here: Patch 1.2.1 changes to rare/rare MI drop rates (vendor farming is nerfed)