There's no need to start assuming that anything complicated and intelligent must be based on some sort of life-form and it's definitely a bad idea to think of it in terms of Earth-based life. Words like "gender", "DNA", and "species" have no relation to this.
All of the seedlings have the same exact design, just different loyalties. This is evidenced by the fact that it's possible to conquer an asteroid and take over the existing Dyson trees and developing seedlings without destroying them. For the people that can only think in terms of genetics, the shape of the seedlings would be like a phenotypic
trait, not a genotypic one. The argument about reproduction competition between seedlings of the same loyalty is void as they are all identical. In this situation, any mutation at all would have negative consequences; the machines are pre-built for optimal functionality. Genes and genetic selection do not apply here.
If they wouldn't behave like us, then the game would be extremelly boring. Again, this is all in a context of a game and players experience. (And it is pretty hard for me to imagine a life form or life cycle that is not based on some sort of control or a fight.)You don't need evolution-based life for complexity.
If you think of dysons as tools like computers, it cuts off implementation into the game design of such wonderful inter-species interactions as amensalism, commensalism, inquilinism, mutualism, predation, parasitism and symbiosis. (Example usage: predation - organisms that are higher in a food chain than dysons, spawned randomly in the beginning of the game, attack and eat lonely dysons, flee when attacked in large groups and so on.) Defence seedlings would the type of seedlings that specialize in autothysis (suicidal altruism) etc etc. And the best part is that if you implement these into any game in any order, they will be mutually congruent with ech other.
Simply put, the more game play mimics real world the more exciting for a player that is.
So anybody has more ideas how to bring more depth to the game play?
Saying that thinking in terms of a mechanical construct limits the design is silly. Think about it for a moment. Where will this game's simulations be run? On the computer.
Building a predator-like machine would be theoretically even easier than building a dyson; it doesn't have to be able to mine asteroids and make trees, just consume seedlings.
How does explaining defensive trees as altruistic change anything about their behavior? That's what they are and what they are made to do. You're just explaining the same thing in different terms.
Also, while computers may not have some of the interesting flaws that life does, they have their own flaws which could result in other interesting mechanics.
For example: Build a launchable radio jammer that temporarily disrupts an asteroid's communication with the master. All seedlings within range would be unable to recieve orders and would be unable to tell friend from foe so they would not attack any invaders. This would last until the jammer runs out of power and shuts down or, optionally, the seedlings will automatically attack any jammers they see.
Another example: Hacking. Capture a seedling without destroying it and steal its faction's public key
code. This would allow you to tap all of their communications to get their asteroid discovery maps and see orders being dispatched for a limited time. If you have enough trees/seedlings (computational power), you might be able to crack the private key, which may allow you to send false orders, cause some to self-destruct, or even take over the entire faction.
Keep in mind that this game is a visual abstraction of the conceptual replicating miner machines. The factory's appearance as a tree doesn't necessarily mean it's actually that shape and certainly doesn't mean that it's biological. There can be more complicated things going on behind the scenes that are not displayed because they're not relevant and don't affect the gameplay.