I thinks it's the roofs that are slightly different, but you'd think that Hornby would go the extra mile to fill the gaps in the range of modern coaches especially as there are currently no alternative manufacturers.
I've just ordered one of those half price EFE J94s from Rails and I was wondering exactly where the real "Amazon" used to run and came across this interesting picture...
Earlestown 1961 by Eddie Bellass.
In their last few years they did pull the Trans-Pennine trains which were usually made up of MK2's so there's a good chance that they did, although they may have been the 2a/c types.