Your house is unusually new to be experiencing such a problem. It appears that it is, at least in part, due to flawed construction. Your contractor apparently did not install an adequate attic ventilation system. Moisture from within your house appears to be flowing into your attic and condensing on the plywood roof decking during cold weather. Such condensation and plywood provide an excellent substrate/environment for mold growth.

I would suspect that the black mold growth is dominated by species such as Cladosporium and not the toxic mold Stachybotrys. You may wish to confirm this from transparent cellophane tape samples prior to remediation activities that would disturb mold.

Since airflows in a house are almost always (though not always) upwards, mold in your attic is less of an exposure concern than it would be in your house or basement. It may come down through bathroom exhaust vents and around light fixtures.

Only if the mold infestation were severe (particularly if there is structural damage) would I recommend re-roofing. If less severe, I would have a restoration company (people who do post fire restorations, e.g. Paul Davis Restorations) scrub it with bleach, allow it to dry and spray paint it with mold-inhibiting paint.

If you have cellulose attic insulation, I would have it checked for signs (mold odor, visible mold) of mold infestation. If infested remove infested insulation (such infestation may only occur in pockets). Whether your insurance company covers mitigation/restoration costs depends on the adjuster. Some accept it without question. Others would be reluctant. If there is physical damage to the roof, your chances are higher that your insurance company will pay for the costs of re-roofing or whatever restoration needs you have.

Re-mediating the mold infestation problem is only treating the problem and not its cause. You need to engage a contractor to install an attic ventilation system that will provide for your house's needs.

A significant question is where is the moisture coming from in your house? Is it from poor site drainage conditions? If the latter is the case, there is a likelihood that mold infestations may exist in other areas of your home.