But it can fly through the hole there... I thought you meant the new 3x3x3 bedrock room in the updated nether map, that has the ultimate prize in it
I'm still using the old nether-map... but now I might want to look at the new one... hmpf.
But I guess I won't, since I looted all chest already and resetting the nether would feel like cheating for me, with all the new loot. ^^"
[edit]
About "flying through the hole":
The wither tries to get the direct way to you, so if you stand behind one of the pillars it's getting stucked right at the other side. So you just have to move a bit to the side, hit it and fast hide again before it can reach the hole.