Currently modders are not able to override Projectile class/entity materials, because both Projectile Model and Cartridge Model accepts only .xob's with baked-in materials. In other cases, - for example, in BaseLoadoutClothComponent you're able to override clothing materials by using GenericEntity-classed prefabs with MeshObject component where you can set your tweaked material (so, ItemModel property accepts both .xob's and .et's).

Proposed solution:
I suggest to allow usage of prefabs in Projectile Model and Cartridge Model properties in Projectile class/entity type.