My QoL suggestion is to have an option where the user can select two blocks/positions in space (either through keyboard or mouse), and a rectangular prism/cube is formed between them that becomes the prefab region.
This would essentially be like a 3d selection tool for creating prefabs/prefab boxes.
This might be slower in some use cases, but could speed up the process for some scenarios, especially for using prefabs to delete large amounts of blocks where visibility is low.