Your question might be mixing two categories - cap exempt employer and cap exempt candidate. The NGO will be a cap exempt employer. By working at this place, you don't become a cap exempt candidate in future. Cap exempt candidates are those for example who work for Company X (non cap exempt) for 2-3 years, maintain status, leave country and then wish to come back either to the same company or a different one. So if you spend three years at the NGO or any other company, maybe return home or to a foreign destination, then you do become a cap exempt candidate.