As I understand it, each material the party picks up is distributed randomly and independently--the fact that you got rocky cores doesn't make you less likely to get any other 4-star materials the party picks up. So lowering their star rating would just make them even less valuable, because NPCs would pay less for them.

The values of materials to other players is driven by supply and demand. Rocky cores are worthless because JK runs are popular, so everyone is constantly picking them up in the Jelly Palace, increasing supply. Warp dust is expensive because people don't fight wolvers as often in tiers 2 & 3, and because it's used in popular recipes, particularly ash tail/skolver/vog cub armors.

If you want rocky cores to be "better balanced" with other crafting materials, you should be campaigning for the introduction of more equipment that uses them as a crafting ingredient, the introduction of new tier 2 areas that would attract players away from the Jelly Palace, and/or a change to the gate generation rules that makes the Jelly Palace show up less often. These things would increase demand or reduce supply, making their price go up (though probably not for a while, considering the stockpiles many players undoubtedly have).

Personally, I think it's fairly ridiculous that 50% of all stratum 4 levels are restricted to only 2 of the 10 possible themes, especially when stratum 4 is the only place for knights to look for the 4-star crafting materials they need to gain tier 3 clearance. I'd like to see the Jelly King and Roarmulus Twins show up less often. Preferably with new bosses (in different themes) to replace them, but even if we just got regular gates to take up the slack.

There is no reason that EVERY boss needs to be available at ALL times, and it does seriously skew material distributions in tier 2.