First off: I have lived & worked in Munich and done exactly what you describe (now live in the countryside working for a remote company) but it is still only a minority of people who [can] do that. It is certainly not the case that everybody is doing it. The ecosystem is alive and well.
In my various data sources tracking job advertising, Munich has been and continues to be where almost all of the interesting jobs are based in Bavaria, and I'm not seeing falling real estate prices at all.
> Munich is the embodiment of the Bay Area in Germany
I'd argue that in many ways it is worse than the Bay Area in the sense that the pay-differential, though in existence, is not nearly as pronounced. Stack Overflow keeps pestering me with emails about jobs that it has classified as "high pay jobs" for Munich. The salary beneath those job ads is usually something like €80k/year before taxes (which are extremely high in Germany). This must seem like a steal to a company like Apple. And this is in a city that has one of the best technical universities on the planet, an extremely vibrant engineering scene, and offers a better quality of life than the Bay Area at lower prices to any senior Apple executive who might want/need to move there from the Bay Area. -- My initial statement holds in that this is a "special opportunity" for Apple, that must be worth capturing for them.