In a related work, the author developed an approach to support model-based system engineering (MBSE) which ensures the conformance to a standard metamodel such as UML, SysML, or NAF, with dedicated project ontologies in order to ease the understanding and creation of models. The proposed mix approach brings flexibility and opens perspectives to support MBSE via predefined templates. However, the usage of specific ontologies, handled by distinct stakeholders, yields to new consistency concerns. The present paper aims to extend this approach in order to support the continuous alignment of those ontologies against reconciliation constraints defined between them. Such constraints deals with semantic relationships which allow for understanding how different perspectives overlap. The approach extension is presented from a user perspective and then theoretically formalised to pursue the purpose of a strong foundation that drives the understanding for limits and constraints in concrete applications.