It's both. Improved coatings will certainly help to reduce reflections from lens surfaces. The best coating is nano-coating since it eliminates reflections almost completely, but these are fragile and expensive, so they are only applied to selected internal lens surfaces where they will make the most difference. Reducing reflections from one surface which would otherwise be a major source of flare or ghosting can make a big difference since it also eliminates secondary reflections from other lens surfaces which could reduce contrast etc.
However, some lens designs are simply more prone to flare than others. For example a rear-facing concave lens could easily focus light reflected from the sensor back onto the sensor, producing one of those flare blobs of light you sometimes see. The spacing and curvature of lenses can make a big difference. I am sure lens designers take this carefully into consideration, but it could be a trade-off between a lens with better resolution, field curvature, distortion, and less/more flare.