My idea is like this: I would like to have a tool that when selected, displays a panel with a series of buttons and a Preview Apply and Cancel button. When in this mode, an orange border would be displayed (like the green border in isolation mode) lett you know. Selecting an item while in this mode would display a grid pattern like the transform tool around the boundary box of the item. Selecting one of the nodes in the grid would establish a setting for that element. Clicking a second element would allow you to select a different node on the other element. In the panel, all elements and their reference nodes would be listed.
If you click the Preview button on the panel. all items become ghosted and clones of them align by their selected reference node. Clicking Apply aligns the elements by their reference nodes, exits the tool and returns to the normal editing mode (like exiting isolation mode).