The programmer runs the generator, which outputs some file(s) with code, which the programmer proceeds to edit: some areas, removing others, etc. Then for some reason the input to the generator (in your case, the permissions) or the generator itself change, and so it has to be run again. Now the programmer is left with the task of having to merge all the changes made to the original files with the new generated output. Alternatively, the programmer says "to hell with that" and updates the code manually instead of using the generator, in which case the tool was useful exactly one time.
As PaulHoule correctly pointed out, though, there are many exceptions to this; generally, if the programmer has no reason to manually edit the files, then the problem is avoided. In some of those cases, though, there's no point in generating textual code, which will then be converted to some other format; you can output that format directly.