[pbsd]

You're mixing modes of operation with compression functions. A mode can be shown to be unconditionally resistant to length-extension attacks. Every SHA-3 finalist's mode was shown to be 'perfect' (indifferentiable) as long as the compression function remains strong. So if a length-extension attack is found on hash function H, this means that something has gotten horribly wrong and it is likely that more serious attacks are also possible.

It is in the compression function (resp. permutation) that Keccak differs the most from BLAKE. BLAKE is ARX-based---like SHA-2---while Keccak only uses bitwise operations. Since SHA-2 is not being deprecated by NIST, they figured that having a 'different' SHA-3 would hedge their bets against an attack against ARX primitives that could potentially break both SHA-2 and {BLAKE, Skein}. This is stated in [1, §3.4]. This has nothing to do with the MD structure.

Sure, when discussing these things security does come first. But all of these functions have been thoroughly vetted already, so the differentiators are elsewhere: sponges are flexible, BLAKE is faster in software, etc.

[1] http://nvlpubs.nist.gov/nistpubs/ir/2012/NIST.IR.7896.pdf