Yes its a connected system, and you have to look at the whole system including the rider.

Lets say for the sake of an argument you have two bike riders with identical leg strength but different leg lengths. Lets say they both have the same thigh and lower leg proportions. Due to the lever of the thigh bone, the rider with the SHORTER leg, will be exerting more force at the knee but with slower leg speed at the knee. The rider with the longer leg length will have less force at the knee but with greater leg speed at the knee.

The lower leg is effectively a connecting Rod (Con Rod) connecting the thigh to the cranks.

It balances out. Riders with shorter legs are capable of pushing gears that are effectively bigger, and as such, shorter cranks are not a disadvantage in any way.

What's needed here is parts that match each other, just as in a car engine. You don't put V8 Con Rods in a 4 cylinder engine. You don't put a crank the dimensions required for a 7 litre V8 in a 1.5 litre 4 cylinder engine.

Humans are much more flexible than a car engine so we get by with things that don't really suit us but even humans are better off when things are the right size for us.