The intensivity of a variable doesn't depend on the homogeneity of the system.
Consider system A, a metal rod of length 2 with a gradient of temperature :
This metal rod has an average temperature, which you could calculate.
Now consider system B, a metal rod of length 4 with the same gradient of temperature :
This metal rod also has an average temperature. Furthermore, it is the same temperature as system A. (if you are unsure about that try to pick a gradient (I arbitrarily chose T = exp(-x) and T = exp(-x/2) for the graphs) and do the calculations yourself)
System B is bigger (it would be twice as massive) but its temperature is the same. Ergo the temperature doesn't depend on the size of the system and is an intensive variable.