Well, just to chuck a few other things out there... VW can call the shots with brands it owns, which includes Porsche AG... but VW AG is 50.7% owned by Porsche SE Holding Company... 75+% of which is controlled by people whose surname is Porsche... so it's not beyond the realms of possibility that Porsche will still do whatever they want without it affecting Audi too much.
As for competing with itself in other disciplines,..
If you're going to sell customer cars, it's a good thing... you make money from each Porsche GT3, Huracan GT3, Bentley GT3, and R8 GT3 that you sell, and it gives great brand exposure, without necessarily being directly linked to a factory effort.
If you're going to run a full works team, it makes less sense, you just end up spending more - which yes, can be put down to a "marketing budget", but unless you field two teams with the same car underneath the bodywork, you're just going to be spending a truckload of money to compete with yourself... the only real benefit in which is covering your bases and increasing your chances of winning through shear weight of numbers.