Why does the 2.5 have lower gearing than the 3.0 then? If anything, the torque peak is lower on the 2.5 -- certainly this is supported by the fact that the 2.5 produces less BHP per litre than the 3.0. Official figures for the x25xe are 227Nm at 3200 RPM, and x30xe are 270Nm at 3400 RPM.
So all else being equal (and considering only torque -- they both peak power at 6000 RPM), the 3.0 should have lower gearing than the 2.5 to get it to its higher RPM torque peak quickly, yet the 3.0 has higher gearing. I suspect it's at least partly to do with economy, but I believe the 3.0 would accelerate more quickly with the 2.5's gearing. Hence the benefit of a 6sp -- have the 2.5's existing lower gearing for 1-5, plus an additional 6th for overdrive cruising (say about 2600 RPM at 70 MPH).
Its totaly to do with economy on production cars......you seem to have some belief that 6 speed gearboxes are better on all configs.....you are wrong and particularly in the case of the V6.
You seem to be missing the fact that you will get to the torque peek in first gear almost instantly (whilst loosing traction!), if you then rev it just past the peek and change gear, in the next gear you will be just below it again......and so on.
And of course the 3.0 would in theory accelerate quicker with the 2.5 diff (gearbox ratios are actualy fairly similar)...hence why the 3.0 manuals are no quicker than the 2.5 manuals in real terms.
Remember that the number of gears required has nothing to do with the position of the torque in the rev range......its all to do with the width of the torque peek (or bhp) and on high output engines, as already mentioned, you might throw in an extra overdrive gear.
Also, forget bhp.....torque is the useable power.....if I had an engine with 1Nm torque at 100000 rpm I would have a 190Bhp engine (this is part of the principal used with small electric motors to get output up).
I don't think 6 speeds are better on all configs, just many of the ones where the best of the power is at the top of the rev range, and lasts for less than 2000 RPM, which in my experience is how the 3.0 V6 is. I'm talking about keeping it on the boil during spirited driving, not keeping it in the torque band. Power is where it's at to make good progress, I'm sure we all know the reasons why this is the case even though the engine actually produces the most output at peak torque.
For example, the 2.0 8v Audi I used to own would have been totally pointless having a 6 speed gearbox, as there was no incentive to keep the revs up or even within a specific band -- it seemed to pull much the same whether it was at 3000 RPM or 5000 RPM. Other similar "lazy" engines are likely to show no benefit with closer ratios, but I wouldn't describe the 24V V6 as lazy.
You just agreed with me that the 3.0 would be quicker with the 2.5 gearing, so much so that with the standard gearing it is barely quicker despite a 37 BHP and 43 Nm advantage. So what would be the drawback of fitting the 2.5 gearing (overall, inc diff) but add a higher 6th so you don't compromise the long distance cruising refinement and economy, but get the advantage of better acceleration when pressing on?
On your last point, torque may be what the engine actually produces, but BHP is what actually accelerates the car. I can reverse your analogy -- if you have an engine that produces 10000 Nm of torque, but could only turn once a minute (1 RPM), you'd have to gear it so high for it to actually move the car at any reasonable speed that it would be chronically slow accelerating (1.9 BHP actually)

As said before I like a nice blend of torque, but also some nice top end. So basically a decent torque curve throughout the rev range, that is maintained enough at high revs to give good peak power. Hence why I'm not so keen on most 2v/cyl engines -- poor top end -- let alone diesels!