The reason for this dates back to the origins of the DIRSIG model, which was originally written to perform strictly in the thermal infrared region of the spectrum. When the model was extended to the reflective regions of the EO spectrum, the concept of using emissivity as the primary optical property remained. The model assumes that surfaces are at thermodynamic equilibrium. Therefore, Kirchoff's law holds and the reflectance can be computed as 1 - emissivity.
In DIRSIG version 4, the user will be allowed to supply either reflectance, emissivity or both.
This is another case of historical precedence. The transmission capabilities where originally added to experiment with path length dependent changes in transmission. Therefore, the model expected to be supplied extinction coefficients. When the model was extended to model transmission for path length independent transmission, the existing support for path length dependent transmission was reused and hence the need for extinction coefficients.
In DIRSIG version 4, the user will be allowed to supply a spectral transmission curve for a material.
This is yet another case of historical precedence. The original capability was added to model large path length objects such as clouds or plumes. At these scales, the choice of kilometers as the normalized path length is not unreasonable.
Unfortunately, the answer is "No". At this time, there is not a standard taxonomy used to define the material ID system. Therefore, a user "A" can create a material database where material ID #1 is a variety of concrete, and user "B" can create another database where material ID #1 is a variety of grass.
Since there is no standard set of material IDs, the user can create a new material with any unused ID number that they wish.
If a material database file contains two or more material entries with the same material ID, the last entry will be the one that is used. At the present, no warnings are given.
The Geometric Database File has a material ID assigned to each element (facet). If the user that supplied the GDB file does not also supply the corresponding material database file, then you have to make an educated guess. Within the GDB file there is also a material "name" field (see the section regarding the format of Geometric Database File). If the file was carefully constructed, this name will be meaningful and you can create a material database file for the GDB file.
To avoid these problems, when another user gives you a GDB file, make sure that they also give you the corresponding material database file.