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Starfinder takes place in the same universe as Pathfinder (probably; history in Starfinder is weird), but several metaphysical things in Starfinder are different. (Also, you know, practical things.)
Regardless, in both systems, creatures do not have memory T cells; you make the same saving through the first time you get bit by a dire rat with filth fever as the thousandth time, even if it is the same rat biting you. The vaccine is also made with Starfinder hypertech, so I don't know that we can say that it works anything like the conventional term; it might just be some very-narrowly-tailored nanobots that do what a conventional immune system would do, if people had immune systems instead of Fort saves.
I actually checked the SRD, and I found exactly one reference to vaccines in first-party Pathfinder materials: the drug Gossamer Veil (https://www.d20pfsrd.com/gamemastering/afflictions/drugs/gossamer-veil/), which, amusingly, has the following description:
Again, the world of Golarion has entirely different mechanics for disease, but more than that, it has entirely different social institutions, built around gods as observable and present as Elon Musk is in our world. "Why the fuck aren't your priests of Jesus healing the sick, as is normal and natural? What is wrong with them that they can't perform the simplest duty of a good cleric, and channel positive energy to help people?" should be her starting point. And because she is literally the alternate-life of a goddess, she should find alchemical ways of preventing disease sus as fuck, because in a world where you can go to any good cleric and get any conventionial disease cleared as long as you are not actually physically dead, not going to goodly clerics to get that care is sus as fuck, unless you're in a part of the world with unusually low access to goodly clerics?
And you know what people generally don't have the training, infrastructure, and general capacity to do in those parts of the world? Become paladins!
Now, I am just going off of the standard SRD and Archives of Nethys as a backup, so if there is a solid reference to vaccines in Pathfinder proper, I may be missing it, and if you know of one, I'd be happy to hear it. But regardless, even if they worked, they would not work as an extension of how people understand how disease works, because in Pathfinder, barring there being a specific Milkmaid background trait that gives a bonus to pox-related illness, you can't observe "Hey, milkmaids and other people who work with cows tend to get the lesser-in-lethality cowpox and tend to be more resistant to smallpox, I wonder why and if we can replicate this somehow." What there are are people who can fuck around with the wrecked space shit in Numeria and maybe get some stuff partially right, but much more likely, what you have are (as we, ironically enough, do have) demon-affiliated fuckers preying on people's hopes that there is a reliable way to handle disease other than divine magic. (Or, like, alchemists or other use-the-spell-mechanic fuckery.)
I don't think you can assume that lintemande's Golarion is identical to the Pathfinder version, although it is based on it.
Iomedae and Alfirin learn about vaccination in America and I think it is one of the technologies that they attempt to introduce to Golarion in a later thread in the series.
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The vaccine rules I quoted are from the Archives for Pathfinder 2e here:
https://2e.aonprd.com/Equipment.aspx?ID=773
My alchemist was crafting them in a campaign I am in which is how I knew there were rules for crafting vaccines. In order to take some pressure off the cleric if we were already immune to the disease we knew we were going to encounter.
Though they may have been invented post Iomadae's ascension, It seems probable natural immunity exists in some form in world but is just abstracted away ruleswise otherwise. As it isn't fun in game to track if your character should be immune to filth fever as he caught it 6 years ago when trudging through a sewer in Alkenstar and was bitten by a direrat or whatever.
Its also possible the varying dieties of disease alter them every so often to evade natural immunity. That might be my take as a DM. That diseases are viral or bacterial but they also have divine forces creating new variants. Golarion does have Anthrax, Dengue fever, cholera and bubonic plague, malaria and TB for example and they even talk about the lymphatic system so mundane diseases do seem to operate much as we would expect here and given the lymphatic systems purpose it would be odd if humans didn't have the same immune system and thus could get immunity to cow pox or something. Its just not an exciting part of the game system to talk about.
Ah, I haven't touched PF2E at all, so that explains it. I guess it will be really important to find out what actual rules the fic is operating under.
The vaccines look interesting, but also not at all like something that naturally would interact with an immune system; how would they work if the lesser ones only work for 24 hours? Maybe they're just releasing tiny alchemical homunculi into your bloodstream.
Re: diseases being updated, you could presumably slap a bunch of dire rats in an Antimagic Field to detect that and study the effect, which sounds interesting. If you want to run your setting that way, you might have an entire laundry list of effects the gods need to personally micromanage to keep the Prime Material from falling askew, and introduce some interesting effects when adventurers go off-grid themselves.
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