These are warnings that point out various possible design faults. The company should know what the minimum spacing they can do, etc. for instance, so they should be able to tell you whether they can manufacture it or not. Many times, certain DMF warnings are ignored on purpose, for instance, if you know that two holes for pin-through components are too close together and you also know that it is inside your manufacturer's margins and the components do not collide in real life within those margins, you ignore them. These Gerbers have already produced working boards so if the manufacturer can produce them as they are they will work.
