What I'm describing is primarily a way to look at choices presented to the player. If the player isn't making a meaningful choice between several options, it doesn't apply. So you're right that once we have decided to collect more wood already, and that goal is set, the decision to designate some trees to be cut instead of designating some stone to be mined isn't a matter of cost and utility -- it's just using the right tool for the job. But this isn't really a choice, it's just communicating your intent to the game accurately.
Even on this low level however, if we look at the question of which trees and how many to designate, you start to move back toward where it's possible to do this analysis again. If I designate the entire map at once, I have to micro less, but the woodcutter will be pathing all over the place to chop down trees from the far corners of the map, and might get killed by the river carp. If I designate only near my front gates, I'll have to micro more when the designation clears, but it's much safer for the woodcutter and the hauling jobs on the wood will be shorter.
Designating stone to dig out instead of designating trees to chop might be useful in other contexts, but we don't treat it as having utility here because it has no bearing on the issue at hand. We still do analysis using cost and utility, it's just only done on the subset of the possibility space that is relevant to the issue at hand. You might say that we first assess what tools (strategies, items, choices) are capable of dealing with the obstacle, and then, upon determining that we need a screwdriver, we analyze whether to use the electric screwdriver or the manual one based on the relative merits of each.
To take this out of the strategy game genre, in a shooter, you might know you want to get from point A to point B, but the gameplay is about all the little decisions you make about where to aim, when to strafe, how to prioritize targets, where to take cover, what weapons to use, and so on. At this low of a level, many decisions won't even involve unconsciously "shopping" between your choices, but happen on instinct. You don't consider throwing a grenade at that Nazi, you just shoot him because he's there and you have your Thompson out. But if you die under enemy machine gun fire, it's likely you'll mentally back up and do some analysis of what happened, quickly identifying the problem (an enemy machine gun nest) and considering a couple solutions (charge it guns blazing, lob a grenade, snipe the machine gunner?) then deciding on an approach to take in your next life. The resulting decision to swap out for the sniper rifle and take out the machine gunner from afar was the best choice you had, but it comes despite some costs -- it slows you down, and more dangerously, you won't notice grenades or flanking enemies for a few seconds. This kind of decision isn't consciously economic, but the same basic principles are still relevant in an abstract form.