Both the prereq script and the FreePBX list are equally useful, consider them mutually additive, neither will upset the other and no packages would ever be uninstalled, so “it really doesn’t matter” . the asterisk script to ensure asterisk has all its pieces, the FreePBX list to ensure FPX has all its pieces. They are “mutually inclusive”
If you really want to be anal, you will spend quite a few hours and possibly save a few seconds off an install that you should only ever run once.
If I was you I would investigate why you are needlessly running ‘make samples’ . . . seriously . . . 
to quote innumerable devs from any named discipline, “Use the Source, Luke”