Ah, gotcha. A Core Mod is a special beast that replaces game calls to the core game files with different code. It runs alongside of the game core, not inside of it, so it's not as scary a proposition as it sounds. Generally speaking, if a developer can do what they need by way of Script Mods, then they should probably do so for efficiency's sake and so as not to have to account for the various patch levels and install types that are all current.
In TS3, we can have more than one Core Mod as long as they don't both or all try to impact the same functions. AwesomeMod conflicts with XCAS, for example. The two NRaas Core Mods don't conflict with anything that we know of.
Other games probably use the term Core Mod to mean something slightly different or have different restrictions on them, like for example, you can only use one.