I agree that would be useful. Unfortunately that would open a whole can of worms and I don't think it is worth the considerable effort. As soon as I allow multiple selection I have to rewrite code all over the place. All the context menus, copy, paste, drag-drop etc. would need reworking on both the main tree and the bin. Maybe in 2.0 haha.
Luckily, you can accomplish what you want using the command bin. Just empty the command bin, copy your desired groups to the bin, arrange them how you want, and then click Save-As. Not quite as easy, but it gives you better control since you can reorder, or trim out commands you don't need etc.
note: When you reopen the editor it will open the original bin again, but you can open any command file in the bin either by clicking "Open a new Bin file" icon, or by dragging the xml file over the bin.
Hope that works for you.