Would be nice to be able to make things to be deleted after the current stage. I can see the flags for things to be deleted that I deleted in the next stage, but I can't find a way to add those flags on the stage I'm currently on so they don't show up in the next stage. I'm aware I can create a stage in between, then delete the entities in that stage, then delete the new stage, but it seems like a roundabout way of doing it.

Just to be clear, this is about the "stage deconstruction/delete tool", not deleting a stage, right?

Sound like a good idea. This can be a user setting. I'll add this soon:tm:

Added in v2.3.0!