The difference between a Seed's rarity and a Mutation is that rarity determines the Seed's base value, while a Mutation is applied afterward to multiply that value further, Cosmic and Rainbow being the strongest currently available.

No, not all Pets boost income the same amount, they multiply farm earnings anywhere from 1x up to 10x depending on the Pet's quality and rarity.

No, you generally can't still get rewards from past Season Crates once that season has ended, which is why event-exclusive items like the Popcorn Phoenix hold extra value afterward.

Yes, you keep the Seeds, Pets, and Gear included with my purchase, exactly as shown in the listing.