Your facts are ruining the the idea some people have that Voyagers were the first trains not to feature perfectly lined up windows
Yes non-alignment started with Mark 3. Some people never did like it. The contemporary French Corail stock has perfect alignment.
Whether alignment is possible depends on the bay dimension. Mark 1 was 1.93 in third class. Mark 2 was 1.95. Mark 3 is 2.1, which was chosen for the first class seat spacing. Class 158 has a bay dimension of, I think, 1.75 which is a bit tight. Electrostars/Turbostars are 1.80 which is just about OK, so the end cars on the most of the various sub-types of Electrostars have pefect alignment and mostly 2+2 seating with table bays. Class 180 have a bay dimension of 1.90. If I recall the BREL International also had a bay dimension of 1.90 (
it had nine windows instead of eight), the difference between first and standard class being 2+1 and 2+2 seating.
A small difference in bay dimension can make a big difference to the overall layout of a railway vehicle as there are typically nine bays in the length of the carriage so it adds up. 1.90 metres appears to optimise the trade-off between space and capacity.
A Swedish study showed that 1/3 of passengers preferred airline type, another 1/3 preferred bay seating and the others didn't mind. If airline type seating is fitted then shelves have to be provided for the luggage that could have gone in the space between seat backs. Thus little additional seating is actually gained, unless luggage is going to end up in doorways or all over the floor, which is what happens on the GW refurbished HSTs, the French Thalys and Swedish X2000 trains.
Bay seating looks bad if it is not aligned. With airline seats it is acceptable to have a few obstructed windows as many people these days are happy to sit and look at a screen for the whole of their journey. The Volo coaches actually turn this into an opportunity. The trick is to get as many seats into the vehicle as possible, with about 30% to 40% in facing bays properly aligned and the remainder in an airline configuration with a pitch of between 80 or 90 cm. In theory seats arranged back to back could be lighter as they can be fixed together to make a rigid structure. In practice it does not happen.
Reservation systems should know if "window" seats are not window seats otherwise people who want a window seat will end up sitting somewhere else if they are allocated one.
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Unfortunately, I think most modern train designers think on the basis on how many people they can seat in their trains, rather than those people being able to look out of the Window. As someone once said to me, you pay the price on your train ticket to be taken from point a to point b, the seat if you can get on is a bonus and having a view out of a window is even more of a bonus.
Train designers do want to give passengers the best journey experience but they need to have an input when the bodyshell is being designed ie very early in the design stage when it is more about getting the engineering right. When this goes right you end up with a vehicle like the class 180.