Engine tune has a great deal to do with optimal engine speed on the highway. This includes volumetric efficiency of the engine, as considered to be an air pump. If low end on a given engine is questionable to begin with because that engine can't really breathe at low RPMs, then odds are it will get worse FE on the highway with taller gearing, than with lower gearing.
On the other board I sometimes visit, there was at least one example of somebody swapping in a transmission computer to get an extra overdrive gear for their electronically controlled transmission, and they actually ended up hurting their FE as a result. When I looked at the other engine mods this guy had, I could see why.
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