As my array is only 2d I tried this approach:
For saving:
outState.putIntArray("matrix4x0",matrix4x4[0]);
outState.putIntArray("matrix4x1",matrix4x4[1]);
outState.putIntArray("matrix4x2",matrix4x4[2]);
outState.putIntArray("matrix4x3",matrix4x4[3]);
To retrieve:
matrix4x4[0] = savedInstanceState.getIntArray("matrix4x0");
matrix4x4[1] = savedInstanceState.getIntArray("matrix4x1");
matrix4x4[2] = savedInstanceState.getIntArray("matrix4x2");
matrix4x4[3] = savedInstanceState.getIntArray("matrix4x3");
It works, but I agree that for multidimensional arrays, converting to 1D array seems to be the correct way.