Personally cannot see any reason to dive for the 1000' markers. Sounds like bad practice to me, especially in poor weather.
I reckon the markers should simply be repainted in alignment with the VASIS/ILS touchdown point.
Doesn't say anywhere that I can find, BUT the LDA must surely take into account this situation.
I would be supprised if Darwin was at all landing distance limited for any of the regular civil aircraft that use it. B767 being the heaviest!