The influence of diffuse functions on electron density calculations
The colours you see in the first two pictures are not electron densities, but phases of the orbitals.
The colours of a single molecule could matter if you were calculating the interactions between different molecules (in which in-phase or out-of-phase interactions could matter) but they make no difference between the molecule(s) within the same calculation.
The electron density arises from the square power of a function which is, say, positive in the red lobe and negative in the blue one.
The square power means that there is no difference between blue and red, or + and - (See Born's law). They are just with inverse phase in respect to each other, but they have no other influence on the system otherwise.
You might find in some software packages a "switch phases" button, which inverts the colours.