A lot of older people retire to no or low tax states, many red, to escape the high cost of living in blue states.
As for defense, you put the bases where you have the space, the land is cheapest and the location is suitable. I would guess that would be mostly red states.
And finally, like you, I'm not sure how interstate highways are "distributed" and "traveled" (wear and tear) to account for the allocations.
I think most posters here agree, it doesn't matter where the money comes from or goes geographically, it is too much and mostly unconstitutional.
You beat me to it as far as SS, Medicare and Medicaid spending goes. When people retire, they become non contributors for taxation, and they become mostly recipients via SS, Medicare and Medicaid spending. To the degree that they move to Red states for lower living costs, they tilt the study. Of course, Red state voters would like to privatize SS — so there would be neither tax contributions nor “spending” for it.
As far as highway spending and agricultural subsidies goes, the author of the article misses the point that Red states would be happy to see those disappear as long as taxes were lowered as well, and a free market was allowed to operate. The cost of interstate highways SHOULD be a local expense, as should the cost of farming. As long as there are no price controls, those costs can be paid for by passing them along in the cost of the products.
It is disingenuous to say that agricultural subsidies are “spending” to Red states when it is the Blue state city dwellers that benefit from the lower prices in the supermarket. The same is true of the interstate highways. Good roads lower the prices of goods sold in the cities, whether grown in rural Red states or imported and shipped cross country.
Another point made by some of the posters on the site is valid as well. How many corporations are incorporated in Delaware or some other blue state because that is where their headquarters are (or just better incorporation laws) ? Their corporate taxes will be counted as coming from a blue state even though their operations benefit entirely from spending in red states where their mining, agricultural, or import-export businesses rely on federally maintained infrastructure.