We're going round in circles again. Many solutions to those "problems" have already been suggested in the posts above. Either have different internal layouts for the front and rear trains, or orient them such that the first class is in the centre.
You're right that a 10-car design is preferable than pairs of 5-car trains. The realists however realise that there's a far greater chance of actually getting new stock for the GEML if it's piggybacked onto another order for elsewhere. Ordering 5-car EMUs and putting up with the wasted space is a reasonable solution, even if it's not the ideal one.
The current set of loco-hauled Mk3s is adequate; pairs of 5-car EMUs is better; and a dedicated 10-car EMU design is ideal, assuming the advantages outweigh the disadvantages of having a small class of dedicated trains.
So what about the very small order that Southern have just made? Just because it wouldn't be a massive order of 500 carriages doesn't mean it can't be made. Don't see why the order would have to be "piggy backed".