Mister being behind everything that happens in the Dresdenverse is one of those deeply buried WAGs. That said, there are a number of clues that hint at something more:
1) The aforementioned WoJ: "We haven't really run into anything that could kill Mister at this point." (spoken after Small Favor so includes a number of nasties).
2) When Harry looks at things with his Sight, everything gets colored -- even pure vanilla Murphy (GP) and "the city of Chicago" (TC) show various hues of colors as energies. The
only time Harry describes seeing something
exactly the same while looking at it under the Sight is Mister.
3) Of the three beings who have used Little Chicago onscreen (Harry, Bob, Mister), two of them profess to not know who fixed the model. Occam's Razor leaves the obvious candidate.
4) Before Harry gets Mouse, there are a number of incidents where Mister "coincidentally" saves the day (e.g. he breaks up the first Harry/Susan kiss in Death Masks where Harry was about to fall under the narcotic spell). Afterwards, Mister just lets his minion (Mouse) deal with those issues.
5) The obvious deference that Mouse and the Za-guard (and Ivy?) show Mister.
---> Clearly, Mister is more than meets the eye.