I think I understand where you're coming from and I can also see how it applies to my little Tri-state area where West Virginia, Ohio, and Kentucky all meet. There's a couple of cities that are geographically right next to each other but have a totally different feel to them with an area right in between that's not clearly of one or the other.
What I'd go with is to ninja up your own way to represent it. I'm not sure what you would feel is the best way to do that, but I do have a suggestion for basically how I'd do it. Read on for more, Captain Kitty!
Go with standard city creation for the New York Capital Region, but also add in one theme for each of the component cities. These would not be quite as important as your overarching themes for the Region and none of them would be Threats as it's more to identify what the city is like, rather than as much as a central point of the campaign.
After that, design your locations and keep in mind both your Regional themes and threats and your City theme. If you can possibly do it, flavor what your locations in Saratoga Springs in a Saratoga Springs bent, but mainly have them tie into the Regional themes. If there's a location that is in a middle zone, you might want to make that clear in the description and maybe make it a semi-focal point of the location. Heck, one of your themes for the Region could be something along the lines of "The Fence Is Everywhere" meaning that there are boundaries all over and some people/places are on one side or the other, and then there are the straddlers. I don't know much about the region for if that would work, but it's a possibility.
You'd end up overthemed, but I don't think it would me much of a big problem because your overarching themes and threats for the region is what you and your players are going to focus on. The other ones are more for local color and flavor, which is possibly just as important, but it's not going to be the drive of the campaign.