The entire point for aperture number is to standardize exposure across focal lengths by effectively changing the exit diameter so that they perform similarly regardless of focal length. While it is true that shorter lenses are faster at any given exit diameter, the aperture number provides an apples-to-apples measure of exit diameter relative to focal length.
Because F = f/d, d=f*F. So what we can say here is that for 50mm at F/1.4 the diameter would be 35.7mm. So for 28/1.4 the effective exit diameter is 20mm. A 20mm aperture on a 50mm lens has an f-ratio of 2.5. So as you can see, the shorter lens needs a smaller aperture to achieve the same f ratio relative to the longer lens. By adjusting the aperture, we compensate for focal length.
It is true that other factors affect transmission, and actually this can be pretty substantial - take for example the Samyang 35/1.4, which is off pretty significantly. In photography, this is not so much an issue because you typically do not need to precisely match DOF and exposure across multiple lenses.
In cinema, however, this is more problematic since your shutter time is often fixed (or in the least far less flexible). This is why cinema lenses are often measured by Transmission Number instead. T-stops reflect the actual degree of attenuation at any given diameter. So for a T-number of 2.0, half of the intensity that enters the lens will exit.