Its not a collective agreement and there is no unified ontology to work from. The overruling factors are consistency of references and context of the submitted article/chapter/book. For instance with dates some journals have it in their style guide that the UCLA Encyclopaedia's should be the yard stick, others prefer dates to be linked to Dynasties. With titles and place names, if you begin with transliterated Egyptian names then those should be maintained throughout the article. If you use Greek names for well known sites then those should be referenced consistently

There is a further element of personal interpretation, one scholar I have worked with refuses to use the words 'priest' or 'temple' (example article) because these are modern interpretations of Egyptian civic roles and institutions, 'loaded' terms - there is no word for 'priest' in Egyptian.

The principal reason behind hellenized names being used for pharaohs is down to a mixture of Manetho and the deciphering of the Rosetta stone. Until Champollion deciphered Hieroglyphics, the greek versions were the only ones accessible. In old books you will still find references to 'Cheops' and 'Mycerinus' rather than 'Khufu' and 'Menkaure'.

With place names, the same applies however there is a further advancement with the use of Arabic place names, particularly in modern archaeological sites. Excavations do not take place at swn.t but on the Qubbet el-Hawa. You visit Luxor (al-Uqsur) not Ipt-Swt or Thebes (that sometimes depends on the tour company).