I will grant that green may be currently weak in some aspects, but you are making statements to the effect that it had no benefits at all, rather then comparatively weak benefits in some circumstances. You certainly seem to think its so bad it should be removed or buffed in some heavy manner. I disagree.
Green codex is mostly intended to be the reliable "safe" choice for less adept players, which you don't sound to be. The necropirates might not spawn/land within your range, and the fight is not an easy one. Other sources of lunatic class gals might not spawn, or spawn without the gals.
The same goes for the medical supplies, they can be quite handy if mission RNG says no academy. Sometimes you can go years without a faction showing, and until you advance a decent way into the game can't you make/buy your own.
Charger laser the same thing applies, not everyone can as easily handle the transition into air game, particularly on the current patch with armed craft much delayed by contacts car thieves being locked behind getting a young uber out of a pogrom, unless you get real lucky with an air race in short distance of your initial base.
So yes, YOU dont get anything satisfying out of green codex, which seems to mean the intent was successful. Go play the other more complex/difficult codexs. And it sounds as if you have and like those better anyway.
Separate point about gems, you can buy them off jack for bounty tokens if nothing else. So can have as many as your willing to throw money at(100k per token. token trade for gems). It may be inefficient but mid to late game if you have been playing well money stops mattering as a limiter and you buyout any missing VIPs and almost all the rare components you could want.
Even if you don't trade jack for them, i rarely run out of gems anyway. They come from many types of missions; mansions, gold freighters, undersea, blood rituals, some units carry them as loot, ect. Now if you get to the later stages and stop doing those missions, well you made your own scarcity by choice. You want real scarcity lets talk shadow orbs.