Not a "problem" to have these shown to us only AFTER the alignment has been choosen... it's just that (to me) it would make sense to always have *all* the available and unavailable (even if dependant on some further choice made - toggle-like) techs displayed on a full tech-tree.
Like i previously said, the GC2 design team probably felt that hiding those would not harm the gameplay "patterns". And, that having them popup like a surprise could be fun. They ARE right. Although, some people may want the real facts clearly spelled out straight ON the interface.
Example; the Germ warfare branch is exclusive to Races with the Annihilator_Super unless you're stealing. BUT... anyone else doesn't get to know this fact from the tech-tree itself and only IF they share the same SuperAbility!

Thus, the invisible edges aren't
intuitively compensated by other similar techs just as Evil gets three new weaponry when Good counters with three new defenses. Somehow, this has to do with the impression we get from research as a whole - and if, partial section(s) remain unknown to us (not discounting experiencing it through multiple games & instinctively REMEMBERING the pseudo-locations of these techs on the
current tree presented to us!) we would not realize the entire scope of possibilities.
Not really serious, just plain simply annoying.
- Zyxpsilon.