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Are you talking about intake or exhaust manifolds?
If your talking about the intake manifold on a TD42 then the main reason people change/modify them is to get more even air flow across the 6 cylinders. Because of the design of the factory manifold cylinder no. 1 and 6 run richer than the other 4 and as we know a rich mixture in a diesel means higher exhaust temps, and high exhaust temps kill. This temp difference can be as high as 50oC. By evening out air flow you even out temps. Also a well designed manifold will allow better total air flow which will reduce spool up times and widen your torque band. It may not make a big difference to your peak power but will help drivability.
For the majority of us with less than 150HP, the gains from a modified manifold, for the expense, are questionable, but every bit helps. But when your wanting to run 20+psi I would think it could definitely be justified, if only for the insurance of not cooking your motor.