With regards to this question, my understanding is that if an auto-entrepreneur registered in France sells digital goods (apps, downloadable software, music videos) to the UK via their own website then they will be subject to the new TVA rules. In short, they must pay the TVA due in the country in which the consumer is located (determined by two pieces of separate information such as an IP address and physical address).
This change is unrelated to the TVA thresholds in any individual country. Therefore, even though an auto-entrepreneur may earn under the TVA threshold in France and under the VAT threshold in the UK, they are still liable for VAT due on distance sales to UK consumers.
In order to prevent individuals from having to learn the TVA rules of 28 member states they can register with the mini-guichet. Information here (pdf) and here. What I can’t get my head round is whether you need to be TVA registered to be able to use this service, i.e. sellers will have to voluntarily register for TVA in order to distance-sell abroad. This is currently the case for the UK equivalent which will destroy many UK micro-businesses selling digital goods in the EU outside of their country of registration.
The only solutions I have found are shipping physical goods (software in CD/DVD) instead of online downloads (likely a short-term solution before physical goods become included) or reconfiguring to sell digital goods via third-party sellers such as Amazon.