Those are just a few examples, but they follow one very specific pattern.

First, they have the category: villa, villa real, real, pueblo. Villa would roughly be translated as "town". This is a technical administrative definition that explains how it is or how it should be organised, what superior administrative divisions they are subject to, etc. Within the category of "villa" there is also "villa real", which means "royal town". This is an indication of whose is the jurisdiction, which in this case it means the town was directly subject to the Crown's jurisdiction (in the case of the viceroyalties this jurisdiction was mediated through the viceroys and the Crown's institutions for practical reasons). Pueblo is a small settlement, what in English would be called a village, and that has fewer administrative powers than a town. A real is a camp, but as it tends to happen, camps tend to evolve into villages and into towns, like the case of the Real de Santa Fe, close to Granada. "Real de minas" means literally "mining camp".

Secondly, you have the denomination, which sometimes can also be an advocation. Spanish naming customs were quite pragmatic, and frequently took already existing names, either of settlements, important peoples, or geographic accidents, and kept using them, that's why there are so many names of indigenous origins in the Spanish America (like Mexico, for instance).

A religious advocation also happened quite regularly, as in Catholicism basically all settlements have a patron saint, something especially true in places like Galicia where the most common and best known administrative division is the parish, and it has been so since the time of the Suebian Kingdom (5th to 6th centuries AD).

But above all, the names you are suggesting are the most formal ones, and nobody ever used them, only ever appearing in some administrative documents. Even nowadays plenty of Spanish cities have some grandstanding titles and denominations that nobody uses, not even the town or village councils, and nobody even thinks the titles and specifications are official. Case in point, my own town: Muy noble y muy leal ciudad de La Coruña, Cabeza, Guarda, Llave, Fuerza, y Antemural del Reino de Galicia (*Most noble and most loyal city of Corunna, Head, Guard, Key, Stronghold, and Bulwark of the Kingdom of Galicia*). The simple official denomination would be Ciudad de La Coruña, but it is entirely pointless to use the denomination of "City" in any administrative matters.

So, all in all what you have is some selection bias combined with some extra formalities that nobody paid much attention to.