Often an impact wrench is used for rusted/stuck fasteners or on something that rotates, and you cannot easily stop the rotation (e.g., a nut attaching the drive shaft to the differential). As you suggest, putting it on the nut is standard practice, as with wheel lug nuts. If there is a bolt head, I usually use a hand held wrench the head. Impact wrenches are not that fast until the nut loosens, then you have to release the pressure. Some people spin the nuts off, I do not like doing that nor is it a good practice in my opinion. Similarly, I do not think they should be used routinely on spark plugs, particularly plugs that are made of 2 or 3 parts (as some Ford plugs are) or when the cylinder head is aluminum (quite often). There are other considerations with spark plugs, so unless you are sure of what you are doing, don't use an impact wrench on them. Another proscription is using them on bleeder screws, such as on brakes, and other small screws. You will likely break the screw.
On rare occasion, such as with bolts that hold the cutting edge on a snow plow, I will use a Vise-Grip or C-clamp to keep the head from turning (they are "plow bolts" and do not have a proper head). Be sure to use proper impact rated sockets on the impact wrench.
I rarely use an impact wrench for assembly. Lug nuts are the one exception, then I use a torque wrench for the final tightening. I have never considered impact wrenches a safety issue. Mine has 3 settings, I, II, and III for removal. I use the lowest setting that works.
On frozen bolts you can help loosen them by adding a penetrating oil and letting it sit for at least 15 minutes or even overnight. Do not do that on lug nuts, they are assembled dry.