Let's be real, that's not an Apples to apples comparison. You Döner shop doesn't sell internationally to various business customers like SW companies do, plus they often involve a lot of tax fraud by not giving receipts to all paying customers and not declaring all profits.
Any Döner shop usually has constant revenue from day one, while SW startups can go a long time without any revenue.
International sales are easy, in most acses they are without VAT and easy enough to file. International slaes, so, have nothing to do with German incorporation but are either EU or whatever driven.
Please correct me, but would a start-up don't need to be a Gewerbe / UG / Gbr / ... to have an entry in the Handelsregister? You can't just make up a "company" a filed it as "Einkommen aus Selbstständiger Arbeit" when doing your taxes, can you?
Edit: Regarding your last point, yes, you can. Upside, it's simple. Downside, you are liable and carrying losses forward is tricky. Among other things.
Also, most start-ups don't need to be registered as a Gewerbe anyway. And let's be honest, if a "start-up" fails to cope with business and bureaucracy requirements your Döner shop successfully tackles daily you might reconsider running a business in the first place.