I do not think it improved it any honestly just made it much longer, in fact I think the Last Supper's noticeably sub par, The Crossing's pretty good but removes any mystery.
It is not like the Prometheus Special Edition; that explains Millburn's behaviour, Fifield's more impressive as a monster, it explains how they both got lost in the structure, and it reinserted that great scene between Janek and Vickers so the fate of the Prometheus does not come out of nowhere, and we actually get more than nothing when the Engineer speaks.
I really had hoped the Ninth Circle Edition might be an improvement upon that. Just without the bizarre audio changes.