If Guardiola plays 4-3-3 against stronger teams
Neuer
Lahm-Badstuber-Dante-Alaba
Martinez
Schweinsteiger Kroos/Thiago
Muller Gotze Ribery
Thiago would be in competition with Schweinsteiger and Kroos for a starting place.
If Guardiola plays 3-4-3 against weaker teams
Neuer
Boateng-Badstuber-Dante
Martinez
Schweinsteiger Thiago
Kroos
Muller Gotze Ribery
As long as Gotze plays as a false 9 and Muller on the right there is a place for Thiago. Lahm and Alaba won't be happy though.
Thiago wants to go to a team where he's a starter virtually every game, so Bayern wouldn't be able to promise him that.