As I understand it - 2015/2446 makes it illegal for an EU citizen to drive a car with non-EU registration inside the EU. If you aren't an EU citizen I don't think it applies to you. Some Swiss hire car firms are laying in stocks of German registered cars so that you can drive them into the EU, but you need to make sure you've asked for one in advance.
Of course many hire car firms charge higher fees if you want to take the car out of the country, with some justification as it can affect insurance risks, required equipment (like making sure it has high-viz jackets, spare bulbs and pocket breathalysers if you're going into france) and potential hassle if you have an accident in another country. Some hire car firms siimply refuse to permit taking their cars out of the country to avoid hassles (as they are entitled to do).
I'm fairly sure I've seen similar situations sometimes when hiring cars in the USA for going either out of the state or into Canada/Mexico - the bigger hire firms are happy with it but the smaller ones aren't.
PDR