The situation at Bayern was that you had two fullbacks that actually started as midfielders and have the qualities to be good midfielders, even if Alaba would have problems with a 360-degree-job. If they had better dribbling qualities or Lahm would have been faster he might have played him differently. And you always have to see Müller's role in the team combined with that, too, as he gave support not just to the striker but to the wingers, too.Pep played the false 9 formation frequently at Barca. It was the role Messi specialised in. The fullbacks moving to midfield was common at Bayern where Phil Lahm became one of the best players in the world.
At City he seems to be refining what he did at Barca and Bayern and achieving even greater heights. We are lucky to be living through this period in football. Pep has re-invented the game but his main inspiration is the Dutch (Ajax) total football of the 70s. It's bloody amazing. The press in this country don't deserve Pep.
I do not think that there is just that "one" system - you have to find ways that match best to the accumulation of players + their strenghts and weaknesse that your team has. As great as e.g. Lahm was - he for sure could not go the fast miles that today often are asked by "modern" fullbacks when speed seems to be the main criteria. But that role at this time was fine to play out his strengths. Pep at that time combined the midfield qualities of Alonso with that of Lahm and Alaba - and you like this could free Vidal to be more present near the box or Thiago to be more in a creative role behind 4.