That's an interesting configuration. Cant see why you could not extend it, a bigger duct is better then a smaller one and since it will connect to the same round one but just higher, you're not changing the amount of air coming in.
Just beware of these humidifiers, they become very nasty if not maintained.
This is what mine looked like when I pulled it out:
I just bought this house, so not sure how long it was in there for.
So if you install one just be sure to check it every now and then. Not sure what type of maintenance they require, guessing the plates need to be changed every 6-12 months or what not. Someone with more experience can probably give a better maintenance routine.