States with significant rural areas, especially southern states, require Townships for local identity and geographic clarity. In Harnett County, NC - where a large portion of my ancestors lived - it matters whether you are from Black River Township or Anderson Creek Township. The Culture is different, the land is different. When it comes to anthropological questions in family history, i.e. "how did they live?," it's significant if they lived in the Township, but not in an unincorporated community or incorporated town within that township. I think it muddies the water to try to 'make' them part of a nearby town when they aren't. I'd vote for being as specific as you can be, especially the farther back you go in time. As we all know, communities come and go, merge, etc. and I think we should document that when we can.
Personally, I feel pretty strongly about having Townships as Categories. Like Chris, I'm a fan of Cross-referencing subcategories. Lillington is in Lillington Township, but also Harnett County, so it shows up as sub-categories in both places. I don't see any harm in that, and there are advantages.