2 stage is for comfort, not savings. So over sizing a 2 stage effectly means you paid for what your not getting.
So it becomes a waste of money.
If you use a massive furnace for quick recovery. You just putting more money out the chimney/flue.
A larger then needed furnace, requires larger duct. More money up front.
If the old duct is left inplace. Then your heat rise across the HX is higher then it should be, and you lose efficiency from that. Your flue temp goes up, meaning more money wasted.
Its a balancing act between size and comfort.
The earlier start, will help the walls and furniture to warm up to room air temp, instead of remaining cooler.
Just because the room air gets to temp quickly, doesn't mean the furniture warmed up that quick also.