From that Mahomes article it seems there is a specific rule that says if the clock is NOT running prior to the snap of the football then a spiked football a spike results in the penalty.
I kind of think you're overcomplicating it from there because conceptually that seems pretty simple to me. If it's a situation such as this one where it makes no sense to spike the football, it results in penalty. You get penalized for being stupid enough to do something you shouldn't do, essentially.