Unterschleißheim is a town in Bavaria, Germany. It is located about 17 km north of the city limits of Munich.
City limits being the operative word here
I suggest you do a bit more research on how regional government and local taxation works in Germany, because that argument is based on a misunderstanding of this. Put In UK terms, you're close to stating that Ealing and Aldgate are not in the same city; a true assertion, but not one that's significant in this context.
Microsoft's move to Schwabing will be a net loss to the local government in tax revenue, as the new offices are in a specially-designated development area, to which lower tax rates apply (for a long introductory period).
There really is nothing odd about this move. Tech companies have been migrating from edge-city office parks to city-centre locations for most of the last decade. Has it escaped your notice how many "Silicon Valley" companies are actually operating from San Francisco now, rather than the actual Valley, 50 miles south of SF? How many UK-based companies have shifted from the M4 Corridor and now operate in London?
The new location is between the two largest universities in Munich. If you knew the city at all, you'd understand why any company that needs to attract smart graduates would jump at this kind of move.