Forgive my ignorance ..... It's often easier to design things the way they always have been designed even though the criteria that made the established design the preferred option are no longer valid. Bear in mind "optimal" also includes packaging considerations. This reminds me of Newey deciding that KERS was an optional item and RB still won a lot of races against cars with KERS.
Perhaps the question could be turned around, why did the other teams think the exhaust configuration that was optimal for NA engine was still optimal for the new engines? The answer should be "We investigated both options and the tubular design gives a marginal gain that outweighs the complexity." I suspect some people actually thought "We've always done it this way" .
Oh, and who's to say Merc have the right answer? Perhaps they got it wrong, or perhaps this is an area where the difference is negligible so packaging rules the decision?