As well as the stick shaker, Dan Air's early -46 fleet, acquired from JAL, had an extra over wing exit fitted at the behest of the CAA. This was to permit a higher seating config. I think Monarch did the same with their 720s. I don't know if either of these mods were required on the -200 but I agree, they would have added to purchase and maintenance costs, whether on the production line or post-production.
BEA neatly sidestepped the Flight Engineer issue with the Trident by sitting a third pilot in front of the panel which also meant not having to deal with Engineering unions in the cockpit. I wonder if this might have been allowed with the 727, had the type been more successful in the UK ?