Answers

There isn't a lot of information, so I'll make some assumptions.  First the black "spots" are on the inside of the roof sheating, the black spots are assumed to be mold and you live in a cold climate?

If my assumptions are correct you probably have inadequate ventilation of the attic area causing moisture to accumulate, condense and probably freeze during cold weather (hence the spots being limited to north side where sun does not directly heat roof in winter) This water probably thaws in the spring and leaves enough moisture at the surface (water activity) for a long enough time with sufficient temperature to allow mold (probably Cladosporium) to grow.

This is probably either as a result of a moisture source, such as a bathroom vent or perhaps ambient moisture escaping the finished area at an attic access, can lights, etc.  I suspect when you added the insulation, the temperature of the attic space was lowered during heating season as less heat was lost to the attic from the finished space.

Probably need to verify that there are no sources adding moisture load to attic, then add or increase the size of the venting or add a humidistat activated exhaust fan to the attic space to correct the cause and then properly remediate the (apparent) mold.

If the spots are on the outside, the addition of insulation may still have changed the balance of the attic temperature, resulting in moisture staying on the roof longer than in the past as the roof is not heated and dried as quickly by the "lost" heat from the inside.  This may mean it is becomes a maintenance issue either by addition of a controlling agent in or on the roofing material or (annual) cleaning to remove the "spots" when they appear.

"Best" is a relative term.  There are certainly options that provide different levels of comfort at different price points.  Recently, we've used a product called Thermal Dry from a company called Basment Systems that installs a over the concrete. It is a snap together PVC product (unaffected by moisture) that has a matte finish(for carpet) or a faux finish (like a wood appearance).  This prevents direct transfer of moisture from concrete to carpet and provides a (minimal) insulation layer at the floor layer.

I am sure there are other simlar products on the market, but this one has served us well.

I'm no attorney-but this is how I understand things as a layman.

Risk is a broad term and I don't know if you are talking to the safety and health or the finanical well being of employees and buyers.

As far as the safety and health of employees there are hundreds of different specific regulations (that carry the weight of law and are mostly administered by the Occupational Safety and Health Administration or a state agency) that address different industries and different scenarios, but as an overall approach the General Duty Clause lays the foundation for pretty much any of those https://www.osha.gov/pls/oshaweb/owadisp.show_document?p_id=3359&p_table=oshact

The "code" reference probably relates to plumbing, electrical, building etc. codes.  They certainly regulate various trades and carry penalties of various types (generally financial or with financial consequences, not criminal) for failure to follow them.

As far as industry guidelines and manufacturers guidelines, failure to follow those certainly expose the builders to potential civil lawsuits to compensate someone for alleged damage as a result of that failure.

If there was a situation that resulted in a charge of criminal negligance that results in injury, then I imagine any of the codes, regulations and installation would be brought in to support (or refute) such charges.

One of the most important foundational elements of a successful fire damage restoration project is the philosophical approach the restorer takes in addressing the damage. Years ago the typical practice was to add oderants (smelly stuff) and try to cover smoke residues with encapsulants (e.g.KILZ). The professional restorer today concentrates on source odor removal, that is, removing the smoke residues as completely as possible rather than trying to overpower them with other "better" smells and covering them up with some sort of "sealer". This is more labor intensive, but is fundamental to restoring the property to a true pre-loss condition and maintaining the property's value. The best bet for successfully identifying what can be successfully salvaged is finding a competent restorer advisor that you trust- this is not really a do it yourself skill. set.