Yep. There was discussion about this among NIST, the Keccak team, and the other cryptographers contributing to SHA-3. The consensus was that because NIST had been involved in the Dual_EC_DRBG backdoor, that their credibility was dangerously low and that they couldn’t standardize anything that ill-informed people could misconstrue as “weakening” SHA-3, even if the actual cryptographers involved thought it would still be secure. So in one sense, you can chalk up the unnecessary computational cost of SHA-3 as collateral damage from the Dual_EC_DRBG backdoor.

The paper is describing what cryptographers have been doing the past 5ish years at least (see various CAESAR contest entries, the forms of Masked Even-Mansour that use 4 or 6 rounds of BLAKE2b permutation, etc.), but maybe encouraging them to push more in that direction.

http://eprint.iacr.org/2016/1188.pdf https://keccak.team/files/Keyakv2-doc2.2.pdf https://keccak.team/files/Ketjev2-doc2.0.pdf