From what I know, the proportions were taken from the red Y (shorter neck), and the greeblie bits show a mixture of red and gold Ys, while it follows the symmetry of the gold Ys (because the right side of the red Y was finished later with different parts).
The head section clearly belongs to the red Y, with a thinner (measuring vertically) nose, the "mouth" doesn´t have the protruding lower lip like the gold Ys, the lower edges of the sidewalls are as wide apart as the upper edges while lower left and right edges should be further apart, the landing gear bay has sharper edges and sits too far in the front for a gold Y and the panel lines and small panels also show the red Y.
So if you want to build a Gold Y, then the MR model is not a good base, if you´re hardcore SS. Which doesn´t mean you can´t make an impressive looking model from it (but a repaint is necessary in any case).