Tools are just tools. There is no inherent good or bad about them.
Take your example of JoinEdge… it is like taping a couple of boards together end to end with duct tape. What are you going to use the result for? If it’s, say, a concrete form made with plywood, joining the boards this way might turn out to be inadequate. However, if the boards are foam core being used as a scenery backdrop, taping them together might work perfectly well for the run of three shows. I have put in nails with a screwdriver, but I don’t recommend it. It kind of wrecks the end of the plastic handle, but it did put in the nail so I could hang a picture. Roofing? I would use a real hammer or a nail gun. JoinEdge can work just fine if you are making a rendered image and fail if you are manufacturing a part.
So, no, the Level 1 and 2 manuals don’t tell you not to use some commands. They tell you what some commands do and give examples of how to use them appropriately.
Also, take a look at the Hole commands, http://www.rhino3d.com/rhino/5/help/en-us/seealso/sak_holes.htm. They also cut out pieces of solids and surfaces.