I do not think it often was a 4-4-2. Maybe sometimes when Coman and Costa were playing on their footwing - but that was the time when we played with fullbacks that filled up the midfield.
And Müller is not a centre forward but somewhat an offensive allrounder - with Pep he filled in various roles - even in one match - from 8 to 10 to hanging striker and winger. And his strength are very unique. Very great tactically, the best player in the world off the ball when it does not mean just positioning (and running) to have own goals but when it is about goals for the team. There is a lot offensives that have an ability to find space for themselves and especially goal chances - but they very seldom do this not in own but in team interest. He is for sure one of Europe's most consistent assist givers from open play and usually scores his load of goals, too. (next season again)
Silva is more a 10, might be able to play an 8/10 - whereas Thiago is a real 8 - can even play a 6/8. You can better compare him to Gündogan than you can compare him to Silva, even if they play lately played with 3 persons in an 8/10 role in the spanish national team - Iniesta, Silva and Thiago. Thiago has the defensive qualities, too, he averaged 2.8 tackles and 4.7 interceptions per match this season. The best in tackles of your team is Fernandinho with 2.5 tackles and Otamendi with 2.9 interceptions (Fernandinho has 2.2).
But - if you compare the systems... Especially in combination with Müller Thiago really acted as a full no. 8 - and Müller even if playing further forward usually takes up more than the usual defensive tasks a comparable player does. I think that is something you should think about - the workrate of the players and the defensive tasks, too. Because you already seem to have that problem when playing Silva and KdB together...