The WWE Championship is the company title, so yes, it's still technically the top one, BUT, if you win the WHC, they're going to treat you the same way as if you were WWE Champion.
Look at Triple H. Half of his title reigns are from the World Heavyweight Championship, yet he's called a 13 time WWE Champion. In reality, he's an 8 time WWE Champion, but that doesn't matter.
At the end of the day, it's really which show you win it on which determines whether it's #1 or #2, they treat the titles the same.