Any extra time spent during a burn is wasted fuel. Intuitively, any time before the rocket is in orbit, some part of the rocket thrust is resisting the force of gravity or else it would fall back down to earth. The longer that time is, the more thrust (and thus fuel) was spent negating that force. It's the main reason why the Falcon 9 boosters do a 'hoverslam' on return and land at close to full throttle - any extra time during that burn is less fuel efficient.

Better fuel efficiency = more payload to orbit = plenty of justification for the extra complexity.

Admittedly gravity losses are more significant at the beginning when the booster/ship are ascending purely vertically than later in second stage flight which is mostly horizontal, but definitely still a factor.

Designing a rocket that's strong enough to survive 100% thrust at maxQ also wastes fuel, because you've overbuilt.

I thought the hoverslam was because the Merlin can't throttle down sufficiently to actually hover?