Excessive transmission noise in car.

[Tony Press]

I don't doubt for one minute that this is correct, but would it be possible for someone to explain to me why the long part of the shaft has to be this way round please. 
I haven't heard this before and wondered what the reasoning is. Would it be to do with the amount that the axle goes up and down compared to the gearbox?

Graham, a so-called 'constant velocity' joint is not precisely so, in fact it speeds up and slows down a little during each revolution. By aligning the front and rear joints in this way, the errors in one joint cancel out the errors in the other. Failing to do so may result in vibration and premature failure.

The 1930's Austin Seven tail shaft universal joints are Hook Joints which give the changing rotation speed needing cancellation as shown.
The later development of the Constant Velocity (CV) joint results in a non variable transition and doesn't need the 'cancellation'.
Earlier Austin Seven tail shafts are fitted with the rear Pot type joint with a similar action to the Hook joint- the front Fabric front 'UJ', because it acts like a CV joint doesn't cancel out the rear joint changes in rotational speed.  
None of this explains your noisy car.