Also, what's exactly wrong in not seeing it all in a single playthrough...? Especially if the restricted content is mostly a handful of very powerful endgame items.
Because I am an explorer (
https://en.wikipedia.org/wiki/Bartle_taxonomy_of_player_types)
and the idea that I'll be unable to view the entire, 100% Bootypedia makes me twitch.
In all seriousness though, I think I understand and appreciate what you're going for. The ghost armor is goofily, game-breakingly powerful, and if you gate it away on some playthroughs then you can add other cool, powerful stuff without making the player into an unstoppable juggernaut.
I think my problem right now is that if you offered me the choice between Illusion, or Destruction+Excess+Communion, I'd probably take Illusion.
My other problem is that the game made me make this choice hundreds of hours ago when I was ignorant of its consequences. The ufopedia entries on the codexes barely, barely imply that your choice will impact your voodoo down the road, and give no specifics. I honestly thought that I was just choosing the paintjob color for my Bonaventura, and went with green because a recharging craft laser sounded handy.
Both of those are fixable through game balance and giving the player more info early on.