For those organisations that teach the: CPL, IR and Instructor courses they have had to be an approved organisation (ATO) but under the same roof some operate as a flying club charging PPL prices for those purposes.. For schools/clubs teaching the private licenses, EASA couldn't make up its mind for may years, many clubs got on with things (wise or not) and also became an ATO but continued charging the normal PPL scale of prices.
An ATO doesn't mean expensive anymore than DTO means cheap. Having said that the EASA has sought at every turn to make all flying expensive. They'l get you whatever choice you make, ATO or DTO.