Are multi-crew operations in a single-pilot aircraft counted towards ATPL requirements?
According to the UK CAA you need:


  500 hours in multi-pilot operations on aeroplanes;


Notice that it does not say anything about the aircraft being multi-pilot/certified for two crew members.

An air carrier can specify in their ops manuals that, for their operations, they require a particular airplane to be operated with two crew members even if it is only type certificated for one crew member.  If their manual is approved, then it is now a "multi-pilot operation" regardless of the type-certification status of the airplane.