The 331's simply aren't fit for purpose for the busy commuter routes that are the Airedale and Wharfedale lines.
Has there been an indication that they'll be altered in the future? The tables are unnecessary beyond belief!
I think you may be missing the rationale behind the new units.
Firstly, Northern needs to increase its revenue dramatically to reduce the subsidy. A way to do this is to make the trains more attractive to off-peak and optional travel.
So the 331s have more space than late 333s to accommodate standing commuter traffic, but the 2+2 seating and the abundance of tables with good window views is specifically there to attract off-peak custom.
And yes, the plan was, and maybe still is, to operate six car 331s on the peak services into Leeds from both Ilkley and Skipton, and 4-car 333s on the routes serving Bradford. But as stated elsewhere six cars cannot start at least until platform Zero at Leeds is completed, at the earliest at the end of next year.
Splitting out the diagrams like this has the added benefit of improving reliability, since at the moment with such complicated diagramming affects the whole circuit.
A study showed that 333s could not be modified with 2+2 seating and added room for standing, so the six car 331 solution is the best available. And don't forget, ordering extra carriages would cost well over £1 million apiece, money which has to come from additional subsidy, i.e from the general taxation pot!