Yes, very safe indeed. It can be quite fun when you are in your 20s, if you live in big urban centers (night life, etc.) - but it's also an impenetrable society. Not being Japanese will place barriers around you in many aspects of the society, sooner or later (even if you are fluent in the language). It's important to be aware of this.
For homicides yes. You can live in Germany or some other European country where murders and gun crime are in single digits per year (haven't checked the latest number, could be higher than single digits but much less compared to US, you get my point).
But the difference compared to Japan is in more petty crime. Things already mentioned in this thread - you can't just leave your laptop on coffee table and go to the loo for 10 min. Or leave your bicycle in front of a store and go inside for half an hour.
As a European I don't think there are many (if any) places in Europe where you don't have to watch your back and be aware of thieves and other (potentially dangerous or at least inconvenient) dodgy street elements.
Add to that overall cleanliness (amount of homeless people shitting on streets, screaming obscenities on people walking by etc, in US and EU cities that will be quite normal, in most Asian cities this would be a rarity) and moving to a place like Japan can be attractive option for people.
Homicide rate seems a ridiculous rate to use; I suspect the homicide rate per 100,000 startup founders is a rounding error of — for example — road traffic accidents.
