There is no balance in the current version. You have legacy fleet (low, mid and high non-phase techs) what was designed as mutually balanced as possible and lives by its rules. And you have new fleet of ships what break said rules. Intentionally, since they are either fleet destroying bosses or "exotic touch" needed for other ship to look "normal". Of course they are hands down better. By design. I see no room for discussion here. We can have endless debate about whats better: Paragon, Onslaught or Conquest but not about this.
Secret ships and the like are explicitly out of balance and shouldn't even be factored in. I don't like those kinds of easter egg style 'secrets'(and they aren't well hidden either) are even in the game, but they are 100% harmless since they dont have any investment cost. I dont have to spend a skill point or dedicate a colony slot to it or something. Mind you I still think it's bad, but it doesn't suddenly drastically effect the flow of the game, unless Alex is using it to consider the difficulty scaling for end-game superboss style fights. That would indeed be trash and be of serious issue. The balancing here depends on how much your required to interact with it. Far as I know, neither the enemy designs for what is effectively post-game or any permanent cost, actually use it. You can ditch them all without sacrifice of any kind.
tl;dr: The existance of the scarab gun in Halo 2 doesn't make the game unbalanced. A lot of things do, but the scarab gun isn't one of the,
With all that said I must add that my point is that current skill system is non-existent because all that "no fun allowed" policy towards legacy fleet. Phase road is like fast track career option you know. You just got yourself your first Afflictor(P) and the next thing you know you are so overpowered that the game have nothing to offer as a challenge. But on the slow track you are getting your bonus armor cut into thirds because it is so important that old ships should be still vulnerable to medium caliber guns. I just can't stress enough how important this all is under Rift Torpedo fire... And since I'm unable to unsee the whole Zig blitz possibility I'm feeling like I'm done with the current build.
Okay if your blaming .9.5 for phase ship balancing then you are way off in another universe. They were a "problem," since way before this new update. Phase ships are extremely high reward high risk ships, for lack of sustainable defenses you get near invulnerability. Effectively, you decide how much flux to use regardless of enemy fire. But, it means you have nothing to small arms, so even light attacks which would mean nothing to other ships, are a drain on your flux, and defending and defending at the same time is impossible. some people have managed that into a such a skill they are effectively untouchable. Using this st a staple of balancing, is like balancing the difficulty of Minecraft mobs to speedrunners like Dream. Phase ships have to be balanced with the AI and general players, not the literal best of the best. If you found a way to use a skill I don't have to break the game, cool. But not everyone can use phase ships effectively.
Now, I have made clear, within my knowledge, why people see success with these ships. I am not one of those people, and if I am wrong to exactly what mechanics and numbers make them so overpowered, perhaps you would be wise to start a thread discussing the ins and outs of phase ships and what specifically allows this supposed behavior. As for the Zig(debating if I wanna go spoiler on that one), it is addressed above. If you cant stop yourself from using an optional SNK boss not likely considered in balancing your opposition, then it's entirely a you problem. You don't blame the scarab gun, for you using the scarab gun.