The combination of AD4 Combat Jump and Seed-Embryo says that Cadmus troops musts use combat jump to deploy. However in Engineering Deck this is not permitted, due to the Inner Area rule. Would Cadmus seeds (and decoys) therefore be deployed in the same manner as AI Beacons, as per Inner Area?
Yes. I would apply the specific exception for AI Beacons to Seed Embryos that possess AD4. The language for AI Beacons is practically the same as for Seed-embryos: "The bearer of an AI Beacon must be deployed using the AD: Combat Jump Special Skill if it appears in its Troop Profile." "Those troops whose Seed-Embryo Troop Profile possesses the AD: Combat Jump Special Skill cannot be deployed using any other level of Airborne Deployment." 'Must use X' is logically the same as 'must not use not X'.
Cadmus is a little different, if it uses AD it must use AD4, but the use of AD is not mandatory so it can still deploy normally.
I initially read it as must use AD. But rereading it that's not actually required... it's just the sense the phrasing conveys. But yeah, if it can deploy normally then do that instead of AD. An exception isn't necessary.