Cantonal costs for maintaining infrastructure is not just based on the population size but also the population density as well as geograpghy. Cities have much lower costs per capita than rural regions. Building roads, train tracks and especially tunnels into mountains is expensive, which is why the mountain cantons usually come out on top.
SH has a high GDP per capita but a relatively low population density which means its costs should be right around average. Which is exactly where it lands in the list.
Nice list of multinational business on that page. Intellectual Property ownership transferred to Schaffhausen based companies, and then charging for worldwide use. That will give a small canton a boost
To me the answer is pretty simple. Schaffhausen has a high GDP per capita for the same reasons as Basel Stadt and Zug: it's area is mostly limited to a single city. Other cantons have more rural areas and smaller towns where there isn't much going on. If you would just count the GDP per capita of the city of Frauenfeld (instead of Thurgau) or city of St. Gallen (instead of whole canton), you would get a similar effect.
Just a small factor in the whole picture then I guess. Why are they doing this? Is there a tax/other advantage (economic or other) at all? Or just snatching EU residence before Brexit?
what's the value of cross-border workers per capita for each of the above? that is what would be relevant in determining impact on GDP/capita, not the absolute number.
Another reason for the great infrastructures of countries like Switzerland, Luxembourg, the Netherlands and in a parallel reality, Ireland: tax avoidance !