I set a stage to hide TFC rock types as PrimalCore common stone, when the player mines the blocks after achieving the set stage, the mod functions as intended, however I noticed that when using TNT the blocks still drop common stone (the block they were hidden as)

mods.orestages.OreStages.addReplacement("generifyrocktypes", tfc:raw/granite, primal:common_stone);

TNT or other non-player things have no player or stage to associate with the action of breaking. This is the intended behaviour.