During the conceptual design phase of an aircraft manufacturing system, different industrial scenarios need to be evaluated against performance indicators in a collaborative engineering process. Domain experts' knowledge and the motivations for decision-making is a crucial asset for enterprises which is challenging to be captured and capitalised. Ontology-based Engineering (OBE) systems emerge as a new generation of Knowledge-based Engineering techniques with advancements of ontology engineering methods and computer science technologies. Ontologies enable to capture both explicit and implicit domain knowledge from historical records and domain experts. These Ontology-based Engineering systems can stand highly complex collaborative design processes involving multidisciplinary stakeholders and various digital tools. This paper proposes a tradespace framework with Ontology-based Engineering features included on top of existing Model-Based System Engineering and interoperability capabilities. These additional Ontology-based Engineering features reuse formalised knowledge via knowledge graph technologies and generative algorithms, changing the cognitive process from the designer, to an automatic process which generates design alternatives for the designer. The tradespace framework is demonstrated in a case study to design the aircraft fuselage orbital joint process, helping the designer to take better strategic decisions at conceptual phase and proving to be an advantageous paradigm for the design process.