So, deep diving into the game's mechanics. Because this is a token there are a few things that don't work for these troopers, and they can be Troopers, namely everything that applies to markers or miniatures. The list which applies to these are... quite something. Line of Fire - the thing that's relevant here - is blocked by Miniatures and scenery with this bullet point "LoF can be drawn from any point of the Trooper's Silhouette to any point of the target's Silhouette without being obstructed by any pieces of scenery or Models (friendly or enemy).". In other words, you can draw line of fire through a mine or MadTrap - or Seed-Embryo. The rules for Decoy state that the Decoys must be considered Models "when a Trooper is replicated in Model form" (italic is my emphasis) however, Seed-Embryo is not Model form, it is a Token so the rules for Tokens (as few as those rules are) apply here. Or should. Technically, Troopers aren't meant to be represented by Tokens as that's meant to be deployables, but as I wrote earlier, I can't really find anything preventing a piece of equipment to also be a Trooper as they're simply not mutually exclusive. As such, my conclusion is that based on rules that are not called "All at Once", you can shoot whatever Cadmus Embryo you want because the Embryos do not block LOF. Where you really need goodwill and to not get stuck on technicalities is ARO. "Even during their opponent's Active Turn, a player’s Models and Markers can react each time the opponent activates one of his Troopers with an Order." See how "Token" isn't part of that sentence? The ARO rules intermittently refers to the Trooper as either "Models and Markers" or as simply "Trooper" so the one thing that's perfectly clear is that Tokens wasn't meant to represent Troopers. On the whole, I'd say that if you want the strictest possible reading of the rules possible so as not to make All At Once do a more than strictly written, you'll probably also have to concede that Embryos can't ARO. And doesn't block LOF. And devalues the trooper something fierce.
Since it's iffy, I would say you can never go wrong with "if it benefits me, it's wrong". Just do something that doesn't make it look like you are trying to pull something over the other player.
I don't understand your rationale here. Just because you see a point on the table at one point in the order, doesn't mean you see it at every point of the order. If a trooper behind another one never existed without the other one existing, you wouldn't be able to see it.
