Hello, this question may not be very easily answered by some as it does relate to programming somewhat.
I assume Load Order tools simply altar a string of bytes containing the last modified date set by the Construction Set to order the mods. If my understanding is right, Morrowind just looks at these dates and loads them in order from oldest to newest.
I am still wondering about the INI Game Files section, I really would like to know if the order of that plays any part in load order maintenance or if it is just to tell Morrowind which files to look at when gathering last modified dates.
Edit: Reworded the question.