I don't think I said they should be equal and framing my point as such seems a bit unfair. I explicintly said:
"It doesn't have to be equal or even better"
But being cut off from the anima tree when the empire path does not do that seems really, really weird. Especially since the game doesn't tell you that. At least, I don't think it does. I'll double check the quest text next time but I don't remember it saying anything about that.
Between the lack of permits, the harder raids, losing out on the empire as a trading partner and having no speech from the throne mood buffs, the deserter path would still be harder if it allowed you to use the anima tree and gave you something else on top of that.
Again, let me clarify that I don't mind that the deserter path is harder. What I do mind is that you're cutting yourself off from a lot of tools by choosing that and some of that seems incredibly arbitrary, which is probably my biggest issue.
This seems quite different from picking a different biome because with a desert or an ice sheet, you know what you're getting into and it makes sense. Having trouble with growing plants makes sense in a desert and an ice sheet. Being denied quests because you got a tribal psycaster in your colony does not seem to follow logically, to me.
Or to look at it from another angle, if i were to do the deserter path, I would feel incredibly stupid if I actually tried to get psycasters like that instead of just recruting a few tribals (or starting as such) and than using the tree. Why would I ever wait for those quests when without even trying I can make so many more psycasters via the tree? I just did a tribal anti-empire run on losing is fun and by year 3 I already have several people at level 6 from the tree. As per the info in this thread, if I had tried to wait for quests, I'd have one guy at 5.
If the intent is that choosing the deserter path means that not even engaging with it is the better move, then I guess it just is what it is. I'm probably never going to play that route again, I was just interested to see what it's like because so far the only thing I saw said about it on forums was that it's bad and nobody should do it and I was quite ready to disagree with that sentiment.