I saw a link to this thread and decided to check it out and chime in with my two bits.
In some cases an intercooler bypass is helpful such as quicker warm up time or trap ox regen. But other than that the only time its helpful is when the boost drop across the intercooler causes less air to be packed into the cylinder than the charge cooling achieves.
Also I would like to add that an intercooler does play a role in improving efficiency. It reduces peak combustion gas temperatures which reduces heat lost to the cooling system.
I don't know about other peoples diesels but on the highway my car generates about 5 to 7 PSI of boost. That raises the air temp about 40 degrees C. More than enough to benefit from an intercooler.
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