Re: Villegas = Villa Egas
The Diccionario de apellidos españoles, which is the most up-to-date and reliable dictionary of Spanish surnames in my estimation, says that Venegas is an "apellido de origen dudoso". Two possibilities are given: (1) "un nombre arábigo formado de la partícula ben-, 'hijo de'" (note the variant Benegas); (2) "un nombre vascuense en relación con el vasco be(h)en, 'de abajo'". There's no indication that the -egas part has anything to do with Villegas.