Unfortunately, Fallout 3 is official, so it's a part of canon. However, the Fallout 3 mutants are different from Mariposa Supermutants, it's hinted even in New Vegas.
While Vault 87 stupid and barbaric mutants are common, (like, official Betheda's statement "Violence is fun! Let's make the game more violent!") , communities like BrokenHills or Jacobstown wouldn't be possible without supermutants using common sense, like Marcus.
Also, Master was putting more capable indivuduums in charge of his armies, like Lou, while Vault 87 mutants are unorganised packs of monsters without leader. And leading armies, or at least, interpret orders, requires intelligence.