Ok... I can imagine 1 small reason why a user would prefer the Preferences window over the Filter composer.
I usually sort all my filters in certain ordered categories right after I create a filter. For advanced users who already know the filter options, this could create some extra troublesome steps.
Though, personally it wouldn't bother me if you locked it to the Filter composer. I already manually open the preferences window to sort Element hiding rules after I composed one.
So this reason is very small and not really important...