I lived in rural areas a large portion of my life. What you are describing is limited to areas with extremely small populations. Meaning even my hometown of a few thousand has a Walmart (put up when I was a kid in the 90s) an Aldi, and two local grocery stores with tons of healthy options.
So yeah, there are a lot of towns that fit that criteria (less than 1000 residents). But as a portion of U.S. population it is not substantial in any way.
i lived in one of those small towns through highschool, just a blinking yellow light and a gas station. What we did, and everyone did, was drive the 20miles to the large town with a Walmart and get groceries there. It only takes 20min because there's no lights or traffic in those areas so the time commitment is about the same as living in a city. My mom made meals from her recipes using basic ingredients so it's certainly feasible to eat how you want in these areas. Only in the most rare/extreme cases are people forced to grocery shop at a gas station.
I've got family in the rural Midwest. It would surprise me if their town wasn't a food desert by these definitions. You might go grab a thing of milk or sliced bread in a pinch at the convenience store, but yeah otherwise you just make the short drive into "the city" to get food at a regular grocery store.
Or you just ate the food you were growing on your own lot, or what your neighbors were growing, or from the farmer selling stuff off the highway.
So yeah, there are a lot of towns that fit that criteria (less than 1000 residents). But as a portion of U.S. population it is not substantial in any way.