SD79 is divided highway (not limited access) out in the flat lands east of the Hills. US16 to Hill City is the main access route to the Faces.
My old copy of S&T takes me up I25, US18, SD89 (US385). That's with 'quickest' set. With 'shortest' most of the WY part is US85.
I'd suggest reviewing the routing options, including the speed estimates.
These mapping programs seldom have special knowledge about routes. They just have the road map from which they can calculate distances. They estimate speed based on broad categories of highways (e.g. freeway v mainline v secondary etc). S&T also has construction info, though whether that affects speed choices, I don't know.
At least on my copy, the only way to alter a route in S&T is to add intermediate destinations. In this case, adding 'Edgemont' should send the route through US18. With Google Maps it easy to drag the route around, adding points. GM also gives up to 3 choices, with distance and time estimates.