Is a tool like Excel, which the vast majority of small companies are currently using, certified? Of course not! You have to pay for special software like Ciel Devis (9 euros/month) or Ciel Compta (9 euros/month). The keen observer will notice that they're produced by the same company, whose former CEO had a stint at Intuit - another software company that is very good at manipulating legislation to push its own interests.
If you get audited and are not in conformity, you get a 7500 euro fine and 60 days to correct your situation.
But what if you are serving foreign clients, and use foreign software to produce invoices that fulfill local regulation? Or if you developed in house software to meet your very particular needs? Heh, sucks to be you, go give money to Ciel.
That being said, the law says that if you do your accounting without software, you don't fall under the regulation. So can you just do your accounting in Excel, copy it by hand, and show that when you get inspected? Who knows.
There are many, many cases like this of useless bureaucracy and regulation in France that make it a nightmare for anyone to start and run their own business. My friends who have been "auto entrepreneur" in the past have hated every minute of it, and most of them have moved to other countries. I'm French, likely to start a company in the next 5 years, and would never go back to France to do it.
The government doesn't really want to create an environment where small businesses can flourish - no one has the proper background to really get what factors contribute to that. What they want is to get the big bucks from venture capital flowing into the country so that they can boast about having a French Google or Airbnb or whatever, which is purely a vanity metric and not particularly constructive for the economy.
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