The word presidio presents some problems for me, because its meaning has changed since came into use from Latin into both English and Spanish. The etymology of presidio – agreed upon by both English-language and Spanish-language dictionaries – is from the Latin præsidium, which means, according to Dictionary.com: “guard, garrison, post, lit., defense, protection,” and Wiktionary (Spanish) “defensa.” However, for some reason, while the primary English definition, “a garrisoned fort; military post,” is arguably quite close to the roots of the word, this meaning is the fourth and fifth definitions found in the Real Academia Española dictionary (4. Guarnición de soldados que se ponía en las plazas, castillos y fortalezas para su custodia y defensa, 5. Ciudad o fortaleza que se podía guarnecer de soldados). The preceding Spanish definitions all relate to incarceration (1. Establecimiento penitenciario en que, privados de libertad, cumplen sus condenas los penados por graves delitos, 2. Conjunto de presidiarios de un mismo lugar, 3. Pena consistente en la privación de libertad, señalada para varios delitos, con diversos grados de rigor y de tiempo).
At some point in time, the word presidio took on a meaning of prison in Spanish; indeed, the words presidio and prisión are synonymous in Spanish. So when did presidio change in Spanish to include the concept of incarceration? True enough, one could argue that being a soldier in a fortress garrison could be equivalent to feeling like one is incarcerated, but I doubt that this is the case. The second English definition elicited from Dicitonary.com (“a Spanish penal settlement”) might well help with some of this question, insofar as implying that the condition might just be something typical of Spanish. (Of course, the word appeared to enter English from Spanish, so this could also just be a nod to that history…)
According to Wikipedia, “A presidio is a fortified base established by the Spanish and Mexicans in North America between the sixteenth and nineteenth centuries. The fortresses were built to protect against pirates, hostile Native Americans and enemy colonists. Other presidios were held by Spain in the sixteenth and seventeenth centuries, in Italy, on Elba and in North Africa.” In this manner, it seems likely that the constriction of presidios was part of a campaign of Spanish imperialism in what is modern-day California, Arizona, New Mexico, and Texas. Indeed, looking at the history of the Presidio of San Francisco turns up a lot of information about the old Spanish fortress (built in 1776), but nothing specifically mentioning a prison.
Investigating the Spanish page for presidio, it also indicates that presidios were built as fortifications for soldiers in far-flung territories of the Spanish Empire, meant to extend imperial power. (“El Presidio era un tipo de fortificación, instrumento de defensa y pacificación territorial, típica del periodo colonial español. En sus inicios era la base defensiva de las rutas y caminos que permitieron la colonización y el dominio los territorios del norte de México actual y el sur oeste de los Estados Unidos.”) However, it goes on to say that many presidios were dismantled (desmontar), becoming a sort of quarry for building materials, with the original footprint of the presidio building possibly becoming a sort of park. (“Al ser desmontado el presidio era olvidado y convertía posteriormente en una población que aprovechaba cualquier resto de construcción abandonada para hacer sus casas, trojes y formando la plaza principal que alguna vez fue el espacio central del presidio.”)
Using this logic, it may be possible that in some areas, presidios were not abandoned and dismantled, but rather repurposed to become prisons; what once served to keep out hostiles was transformed to retain them. Such was the history of one famous example of fortress-cum-prison: the Bastille. Originally created as the “Bastion de Saint-Antoine” in the late 1300s, after the Hundred Years War (for which it was originally built), its impenetrability and proximity to the city that it was originally built to protect made it a prime candidate for a jail. It is quite possible, therefore, that cities built near presidios (or came to encompass one) might well repurpose the fortress in their midst into a prison, rather than build one from whole cloth. Their fortifications would make it difficult to bust a prisoner out (after all, they were built to repel attack from the outside), while also making it difficult for a prisoner to escape from within.
That the name by which they were called didn’t change from presidio to prisión isn’t too surprising, either: the Bastille, while still referencing its history as a bastion to protect the city of Paris from the invading English, eventually came to synonymous with a prison and, then, the many social problems perpetrated by the French monarchy. So, too, the transformation from presidios being equivalent with protection and pacification of far-flung, dangerous territories into fortified prisons isn’t too far of a stretch.