Well, you can do anything you like with your own calculations, but somehow you have to get the coherent phase information which is not included in the Mueller matrix, as it is based on incoherent properties (intensities) only.
The purpose of Mueller calculus is to allow you to describe the partial polarization of a beam of light, and to transform this easily, through matrix multiplication, to simulate polarizing components. You simply cannot get the phase retardance of a coating out of a Mueller matrix as the data is just not in there.
I don’t think you should conflate the ‘generality’ of the Mueller matrix with it being a superior method. It definitely has its role, but the Jones matrix representation of a ray contains more data. You then have to make up the bulk properties of a beam of light by mixing rays of different polarization states together. There is nothing you cannot do with an ensemble of Jones rays, whereas the Mueller approach limits you only to incoherent properties of the beam. I suspect (without proof) that the codes that use Mueller matrices only do illumination calculations with them. That’s not a knock against them, it’s perfectly valid, but it is a subset of the things you can do with the Jones matrix.