Nobles and Alphas should deal the same amount of damage at every difficulty, they deal no damage in peaceful. 99.9% of Pixelmon servers use peaceful difficulty, making this new mechanic nonexistent.
p.s. Alphas should be way less aggressive: opposite from nobles, where you choose when to battle them, they just spawn near you and kill you with 2/3 hits, especially now that they don't have the red aura they are impossible to avoid.
Nobles should use the throw attack more often, they can be easily caged to spam balms from a hole, and would make more sense for them to jump less like kangaroos.
It's possible to place as many feeders as you want, each with its own chance to generate a noble. You should be stopped from "redeeming" a noble from the feeder while you already have one spawned, if you cage the first noble you can literally farm rare pokemon with no efforts.
Once their rarity will be fixed, nobles should also become tied to certain biomes/pokeblocks (i.e. Kleavor -> Jungle-like biome or brown/yellow pokeblocks), so people can prepare in advance and aim for a specific battle.
Just two little rebalances I would suggest for some 8.7.0 features (personal opinions only):