You don't NEED a clean partition for TM, but Apple recommends it.
The block-level copy will work better for the reasons I outlined earlier. If they're too confusing, don't worry, its pretty nerdy stuff. But the beauty of CCC is that it makes it painless.
I really think it will work, and I would test it myself but I don't have a second external drive big enough for my TM.
Is there any specific part of my "argument" that I can clarify for you? I'll try to simplify it overall...
Imagine you're copying a piece of paper. You can either use a photocopier or type it into a computer.
If you use the photocopier, it doesn't care whats on the page. It could be pictures, words, many different languages, etc... it just copies the whole thing.
If you use the computer, you have to be able to read whats on the page and re-type it, not to mention you can't copy a photo, different language, etc...
Think of the block-level copy like the photocopier. It doesn't care whats actually there, it just copies it, unlike file-level, which actually reads each file and then copies it.