The main reason for the 'load 16' is that only a single loco is required. 16 also happens to be the platform length at Euston. At present we send 32 coaches north with 2 locos. Why send smaller batches with more locos?
Plus all the locos needed for the shunt moves and moving the stock around and getting it out of the platforms at the terminals again.
If the lowland sleepers ran seperately you would need an extra Class 90 for the 'backhaul' portion of the journey but you would not need all the locomotives required for the shunts and so on since it could run as a fixed push pull formation directly to it's destination.
Two Class 90s for the entire journey instead of One Class 90 for the whole journey, a Class 90 for Carstairs-Edinburgh, two more electrics to get the portions back out of the platform again and numerous other pieces of stock.
Push pull is far easier to implement with a fixed formation since you can just stick a DVT on the far end.
You could also add another seating vehicle since the platform length at King's Cross is at least capable of 9+DVT+Loco since they do it every day.
If you ran it from Euston you could stick eight additional seating vehicles because you would have a Load16 capable platform to work with.
EDIT:
Platform 0 at King's Cross is rated for 305m.
That means it will fit a DVT, a Class 90 and 11 Mark 3s.
That is six sleeper vehicles, a lounge vehicle and four seating vehicles, with luggage storage being available in the DVT.
That is rather more seating than is available now and would probably improve the economics of service.