grammar - Correct comma use with "but" and "that"

Compare these 3 sentences:

1. Both are based on librsync, but above that they behave quite differently.


2. Both are based on librsync, but above that, they behave quite differently.


3. Both are based on librsync, but, above that, they behave quite differently.

I found the first one hard to parse (I needed to read it more than once to actually make sense of it). The second is far easier, and the third has oh-so-many commas.