The fraction of oxygenated haemoglobin is a parameter which is calculated from values directly measured by absorption spectrophotometry. It is expressed as FO2Hb.
As you can see, oxygen saturation and the fraction of oxygenated haemoglobin are not interchangeable.
Observe this crude diagram, which illustrates the difference between the various measures of haemoglobin oxygen content:
Functional saturation vs fractional saturation
The term "functional saturation" refers to the saturation of the haemoglobin which is capable of transporting oxygen, and corresponds to the sO2. The term "fractional saturation" refers to the fraction of total haemoglobin which happens to be oxygenated, and refers to the FO2Hb.
In healthy individuals, the two values will be very similar, as these people typically have little dyshaemoglobin circulating around. However, the sO2 will be consistently a little higher, because everybody has tiny (~1%) fractions of FMetHb and FCOHb.
This has implications for the estimation of the total oxygen-carrying capacity of the blood. In the presence of large concentrations of dyshaemoglobin, the sO2 will remain normal, while the actual oxygen transport will be severely impaired. The FO2Hb will accurately reflect this impairment.
What is the point of measuring this value?
Which is the more trustworthy of the two indices, FO2Hb or sO2?
The answer is that both are useful in different circumstance.
One must remember that the end goal of all these measurements is the determination of the oxygen content of the blood.
If one does not have the ability to measure abnormal haemoglobin species, one is served with the ctHb value. This value represents the total haemoglobin. The FO2Hb can be used together with the total haemoglobin to calculate the total oxygen content; and one would not need to know the concentration of dyshaemoglobin species.
However, one would not be able to determine the total oxygen carrying capacity in this way.
For that, the sO2 would be the more relevant measure. The sO2 value excludes haemoglobins which have lack the capacity for oxygen transport (it uses oxyhaemoglobin and deoxyhaemoglobin only).