Without knowing the costs to manufacturers of each component that goes into their cameras it isn't possible to definitively answer the question. Unlike manufacturers of other high end electronics (such as the iPhone) who farm out the manufacture of most parts of their products, most camera makers manufacture most, if not all, of the components of their cameras in-house. The imaging sensor itself is sometimes a notable exception. With DSLRs the scaling of products is so much smaller so that a much larger part of the price of each DSLR is the R&D and design cost involved. With other products that sell larger numbers of units, the manufacturing cost is primary because the R&D is spread out over many more sales units.

One thing you can look at is what feature sets are offered at similar price points by the Big Two (Nikon & Canon) and by everyone else. You often see a lot of features available only in the more expensive models from Nikon/Canon that other makers will include at lower price points. In general, you don't see the types of more advanced Phase Detection Auto Focus (PDAF) systems found only in top tier Nikon/Canons put in cameras from other manufacturers priced to compete with Canon/Nikon's entry level and second tier DSLR bodies. They all seem to have the same types of systems with fewer focus points and fewer configurable options. This would lead one to believe either the R&D/design cost, the manufacturing cost, or both are considerably higher when talking about advanced PDAF systems.

The other consideration is that the best focus systems only work at their top performance levels when paired with the best AF lenses. The further from the center of the frame a focus point is, the wider the maximum aperture of the lens needs to be to give the same focus accuracy as the center point can provide with a narrower lens. The more precise feedback a lens provides to the body about how far it just moved the focusing elements, the more accurate the focus system can be. A good set of top notch pro quality lenses far exceeds the price difference between consumer and pro grade camera bodies, so the assumption may be that anyone using the lower grade bodies is also using lower grade lenses that wouldn't benefit from many of the advantages of the more advanced PDAF systems.