I think your problem is you're looking at a eutopian situation where you have enough people for everything - in which case then yes, all options will be taken.
Thats like saying a £1million lamborghini is good value for money if you're a multi-billionaire because you can have a lamborghini and a BMW and both are good.
What we're considering is most scenarios where you have to choose between putting a worker as a scientist or a worker on a tile. And in this respect comparing the value added by using a great scientist to make the improvement, rather than using him to start a golden age or to bulb a technology.
As for the beaker-per-pop, it is in fact 1:1 but that doesnt mean 5 beakers is worth 5 population, simply because the 5 populations' only job ISN'T to make those 5 science but who will also become either specialists or work tiles.