Secret Passage

Minor Rune: Secret Passage

Major Rune: Phase Field

Secret Passage toggles an area between two layouts. Blocks in the world are naturally in the Normal Phase. Activating a Secret Passage rune toggles all the blocks in a sphere around the rune to the Aether phase. Aether phase is empty to start off with. You can place blocks in this phase and the rune will remember them. When you toggle the rune back, all the original blocks in normal phase will return unchanged. To make a vanishing secret door, simply reconstruct the door frame with no door in the Aether phase and then toggling the rune will toggle the presence of the door.

Safety: Players (not mobs) that would land inside solid blocks and suffocate because of Secret Passage or Phase Field will have teleportPlayer invoked on them which will safely move them up out of harms way. This can also be used to create elevators.

Legacy Notes
Phase blocks and Topsy Turvy switches combined. All you need to do to edit your phase blocks is mine them out or place blocks normally. It should be much more user friendly. However, this doesn't fully replicate the movement functionality of Topsy Turvey. For that, I would use an automated Runecraft to turn a construct around 180 degrees. You'll want a frame around the Runecraft made of natural blocks so that the Conductance works correctly.