I spent some more time going through the categories today. First thing, I think that everything you have done so far is completely compatible with the project guidelines. You've mostly categorised people at the level of the present-day municipality, which is really helpful.
The guidelines state: In most cases, it might be fine to use the present-day category for a given town, regardless of when the person was born or died. You've already named the Guanajuato municipio categories in exactly the way the project suggests ... so no need to revisit your 25,000 hand-entered profiles!
The historic, small-town level categories are mostly useful when a researcher wants to dig deeper in a specific town or lineage: "historical categories are useful to divide groups by historical era, reducing the number of people in a category, grouping people who may have lived at the same time, and simplifying the usage of shared historical records, like birth registries, or cemeteries." Other projects (like Acadia and Canada) don't always bother to create every single historic place category. It depends on usage.
But, you note that "there seems to be a distinction of the area before and after August 1821 which is what I use for naming places in Mexico." So yes! You already know the logic of historic names. If it turns out you ever want to use historic categories going forward, I set up historic (Reino de México) categories for the major towns in Guanajuato that already have present-day categories. And I created a couple categories to handle strange name changes (Piedra Gorda > Manuel Doblado).
In a few cases I asked editbot to rename categories like "Ciudad de Manuel Doblado" to "Municipio de Manuel Doblado", to make them consistent. But this won't require any manual intervention.
I hope that's helpful? I've emailed you directly, if you want to chat more.
B
