Great question. This is an ongoing challenge because different parts of a company use terms differently. One rule of thumb is to avoid using terms that have many different meanings across the company – this will just cause confusion. Things can be set up so that local groups can see their own terms in UIs of systems they use, but ambiguous terms are best avoided in the enterprise-wide ontology.
Another factor is that when a number of major IT systems permeate everyday operations in the company, the terminology of the IT systems can effectively become the terminology of the company. Worse, these terms might originally be those of the vendor, not the company. A target to hit is for the terms in the ontology to be readily understood by anyone in the enterprise who a) needs to know what is going on and b) is unfamiliar with terms tied to specific applications. It can sometimes help to start with with long names whose meanings are fairly easy to grasp. Independence from IT systems is important for an enterprise ontology which reflects the stable and essential concepts in the business; IT systems change a lot.