I'm not sure if this would just break the game or not, but for foods try removing [EDIBLE_WHENCOOKED], [EDIBLE_RAW], [DRINK:], and [DRINKVALUE:] from all underground plants. (Might have to add a few others as well, check the list of plant tokens.) Then create other foods that are edible, cookable, or brewable, but are not growable in any season. Finally, create a smelter reaction to turn piles of the former plant product into smaller piles of the latter plant product. You can play with probabilities and everything too, so that you really have to grow a ton of the former to get anything that will provide nourishment to your dwarves. Additionally, you can add in extra reagents, so that it is even harder to get actual food. For example, you could require that you use a bar of iron and 10 plump helmets to have a 50% chance of obtaining a single fortified helmet lump, which would be edible only when cooked. (Don't forget to add seeds as an additional product of the reaction, unless you set your non-growable but edible plants to produce seeds when eaten raw, milled, or brewed.)
Smelter reactions only work with piles, so a stack of 5 plump helmets and a single plump helmet would count the same for a smelter reaction. That may have the advantage of eliminating the planter skill bonus, though.
You would definitely need to add seeds, too, since the non-growable plants would generate non-growable seeds when eaten raw, milled, or brewed. When calculating the total supply, remember that those non-growable seeds can be eaten raw or cooked, providing a (non-valuable) meal component.
Cage traps are unfortunately completely hardcoded, so you won't be able to do anything about those beyond giving everything trapavoid. I've always felt that that's a reasonable solution, since things like spike traps, deadfalls, and death-corridors still work, you just need a bit more creativity when placing them than "80 cage traps in a line here" or "weapon traps over here". Pressure plates, pull lever(r), and friendly fire are likely to result, but it will kill things.