You bring up a lot of good points about how the framing of the tadpole and ceremorphsis has been made more clear throughout the patches. I, and a lot of people it seems, played the first patch, really thinking this phase of the game was going to be a desperate scrabble to put-off a gruesome death, which really messed up a lot of the conversation and quest flags, placeholder though they may have been.
I don't really have too much trouble with the framing of creche quest and the Gith patrol as it is, it's gone relatively unchanged since the beginning, I think they added some business with the artifact, but otherwise we have Lae'zel giving us a clear objective, a trail of corpses you'll probably never talk to, and cowardly tieflings telling you they're bad news; not really anything to help us gauge the trouble we're about to get into. Showing us that the Gith can terrorize a bunch of refugees and a stuttering Fist lieutenant doesn't really drive home very well, emotionally, the stakes of the encounter, unlike what intellectually you should know about a dragon and the Gith.
before leaving the grove (because who would bypass the grove...) you have three equally tenuous ways of getting rid of the tadpole, the Gith, Halsin and Priestess Gut. I think we're expected to choose which one to pursue based on what kind of character we are and which companions we're inclined to believe more. Note that each of these routes lead to map exits and involve large fights, Halsin and Gut at the temple, and the Creche with the patrol.
As far as Lae'zel's credentials, she mentions that creche K'liir has one of the finest libraries in planes at one point, and possibly that the purification apparatus was developed there, of course I'm not sure when you get this dialogue, or if you have to be Gith to get it either, I'll have to play again some.
I think she also has a dialogue about the Gith always needing servants, if you ask her how the Gith will treat you as non-Gith.
The Gith patrol is the second hardest encounter in the EA for me, after the hag, and part of the trouble with the logic behind it is that it kind of reads as a cinematic encounter, something put there to establish a major henchman, give us another taste of dragon, and telegraph to us that the Gith are not to be trifled with and are after you.
also welcome back Neleothesze
