How are you calculating a diff of an encrypted file? I looked through the technical documentation but if it explains it I missed it.
Have you thought about how to quantify this tradeoff?
I suppose you could pad each encrypted chunk so they're all the same size, but then if you don't want to waste a ton of space you'd have to restrict your chunking algorithm to output chunks with relatively similar sizes, at which point you lose some of the benefits of chunking.
That doesn't mean that it's impossible, of course; just that it would require someone smarter than me. ;-)