It expresses the total percentage of energy, and therefore of heat, that passes through said glazing.
A glazing with an FS 42 only passes 42% of the heat from the sun’s rays (39% in direct transmission + 3% of heat absorbed and re-sent inwards by the glazing). The remaining 85 % is rejected, either by direct reflection (30%), or by the absorption and reemission of the glazing to the outside (28%).