Latin Substitute for forename in Baptismal records

Yes, the Irish name Eoghan was anglicized in some cases as Owen [phonetically close to Eoghan] and in some cases as the latinate form Eugene.  Some priests insisted on using latinate or Biblical names and refused to use the Irish forms.  Others used customary anglicized forms like Owen.  Rarely in the 19th century did the priests use the actual Irish names, which would, however, often have continued to be used by the family members and neighbors (at least in Irish-speaking areas).  People usually deferred to the priest's authority in such situations.