% Transmission or % Intensity is one and the same thing It is intensity of tranmission

Transmittance is a measure of the fractional transmitted intensity, normalised to the input intensity

T = Iout/Iin

It is unitless and is notmally expressed as 0 to 1, or x100 as a percentage.

Alternatively, it is expressed as Absorbance

Abs  = -log10 T

This can then be related to the molar exctinction co-efficients, ansd thus the fundamental materials parameters.

Without doing the  notmalisation of Transmitted intensity to Transmitance, this could not be done.

For a practical reasons the  displaying Y axis as %transimttence is useful. By observation of %transimttence you can control the saturation of signal during FTIR analysis.