What makes one bike faster than another when same wattage is applied?
Most likely aerodynamics.  Modern road bike vendors spend a lot of money improving the aerodynamics, especially for the racing top models. Mor for the so-called aerobikes, but even for the ultra=light bikes, up to the point the weight permits.
The weight is not too important on the flats and is less important than many think even in the hills as most of the weight is in the rider anyway.
Tyres will make some of the difference too. Obviously, top ricing tyres will be faster on smooth tarmac. I made a big improvement from the stock Schwalbe tyres to better G-Ones on my gravelbike. But aerodynamics of modern bikes cannot be beaten by tyres, the differences are usually smaller there.
The groupset may be more clumsy when shifting but when the gear is there, it does it job very well. If you want more gears and have the money (which you probably have if you have the Cervélo S), you can buy 105, it will be lighter, but do not expect to be any faster on flats. (I ride Claris regularly. Some would miss the gears, the shifting requires some power in your hands, but otherwise it does the job done well enough.)