As your original post said you wanted manual in preference to the DQ200 but would accept the DQ250 as an alternative you seem to have contradicted yourself.
Packaging goes beyond an existing ability to mate an engine with a gearbox - you still have to fit it in the engine bay, get the accessories to fit around it, get the suspension to suit the extra weight, get the handling to work with the change in COG, roll centre & front/rear bias.
Economy won't necessarily be better. At least one of the tuners has stated that there's a 10% power loss penalty with the DQ500 compared to DQ250. So if your losing 10% to the pavement then it's likely you'll be using more fuel to achieve similar perfomance parameters.
I still don't think you have an understanding of what an engineering rating is. Sydney Harbour Bridge was being used significantly above (130% IIRC) the rated capacity for years until Baulderstone / Aurecon did the upgrade works. It's quite likely that if VW decide that they want to market torque >350nm (which is already artificially limited) from their engines they'll just get the engineers to re-rate the DQ250.
If I specifiied a gearbox with more than 20% torque headroom (eg:<420nm on a 350nm motor) my boss would have my nuts. Fit for purpose is all that's needed because if you overengineer everything you end up with a big fat tub-o-lard & excess material costs.
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