Is it safe to use impact wrench when you try to loosen the crankshaft pulley retaining bolt? Many suggest just that without any concern for possibility of causing the damage to engine mounts, maybe crankshaft bearings, seals etc.. I think Honda produced that 50 mm hex tool for reason. To hold crankshaft safely and protect it from surprises to say at least. Would it be better to use that tool and unscrew the bolt manually. Is there a chance that vibration from impact will cause damage or cause some components to fail sooner?
I wouldn't hesitate using an impact to loosen the crankshaft pulley retaining bolt. The reason for this is because even though there is an impact involved, it is a rotary impact. The crank itself would incur no damage, nor would the bearings. The bearings take a worse beating during normal operation than they would during crankshaft pulley retaining bolt removal (mind you with proper oil flow, bearings don't usually take a beating, anyway ... but that's a different subject.)
With that said, if the engine was in the car this may be problematic. You may not be able to get to the crankshaft pulley retaining bolt with an impact wrench (most probably would not be able to get to it).
Also, you'll noticed I emphasized the word loosen above. The reason for this is, while I would not hesitate to loosen most engine bolts using an impact, I would almost never utilize an impact gun to tighten one. Especially where the crankshaft pulley retaining bolt is concerned. The reason for this is you will most likely over torque it using an impact, which will cause issues for you. Also, you never want to use crankshaft bolt to draw in a balancer pulley, but utilize an installation tool instead. The installation tool will be completely engaged on the threads down to the bottom of the hole inside the crankshaft. This gives it enough purchase to run the pulley/balancer onto the crankshaft without the worry of stripping out the threads. By trying to use the bolt, you'd only be using a few (very few) of the threads, which can cause catastrophic results. Believe it or not, it's very easy to strip these threads out.
Why is all of this important? Because you will most likely need the tool to hold things in place while you are installing the balancer onto the crankshaft.
@paulster2 is agreed with. However in real life it is sometimes necessary to find compromises. Packing a cylinder with rope, putting a lock on the flywheel, and other crankshaft holding techniques may be necessary. In some cases, mechanics will simply eyeball the torque needed with an impact tool, or with an impact tool with torque limiters (these are flexible rods used to get torque correct and are today commonly used on torquing tires).
So sometimes one has to be a bit creative, while not throwing risk management out the window.