Some mod developers try to work around the map generation issue by having random ores spawn from an entity (Think Space Exploration Core Drills for example). Some others use a conversion method, where just putting i.e. iron ore in an assembly machine with a recipe to change it from iron to whatever else ore you'd want.
The latter method is a much less unrealistic method to do it, but makes the mod 100% compatible with a vanilla generated map. I suppose Space Exploration can force regen of the surface to spawn the Core Seams, but that'd give a side effect of regenerating all ores on the map as well.