The Warner Archive version is back in stock at Amazon. It just arrived at my house on August 5 (I ordered it on June 10!).
I can confirm that the version of Mystery of the Wax Museum on the House of Wax Warner Archive disc is indeed the previous transfer, and that the new transfer is light-years better. Most striking differences are that the old transfer has blues in some places, while the new one is accurately two-color, and that the old transfer is very high in contrast which obscures lots of details, while the new one has a beautiful range of shades with full details visible.