With my commute, if the driver takes a(n illegal) left when leaving the complex where I work, the GPS will recalculate and tell them to take the state highway, which is further in distance, but sometimes shorter in time. This is the only time where I get charged more than the up-front quote. If they take a right turn like they are supposed to (all exits from that side of the complex are right turn only), then they take a pretty much straight shot surface road to get me home.
I think Lyft doesn't take the highway route into account when calculating the up-front fare because an illegal turn out of the complex is required to get to that on-ramp.