Though I have played a githzerai monk in 4th Edition and used gith in a low-level Dark Sun campaign (also 4th Edition), most of my exposure to things gith-related comes from Planescape: Torment's Dak'kon, and I am not even sure how much that--or even this--adheres to the "official" lore dispersed within a myriad of Planescape supplements.
While part of the reason I have yet to really use them is that not many games I run get to either the Astral Sea or Elemental Chaos, another major factor is that like so many other humanoid races they are incredibly underwhelming, confusing, and at times contradictory.
Taking it from the top, I guess they used to be a race of evil humans. I do not know why they were all universally evil, but this is apparently significant enough to note. Mind flayers conquered them somehow, for some reason, and bred them to be warriors and bodyguards. This caused them to gradually change physically, and they developed psionic powers that either the mind flayers did not notice, or figured that psychic warriors were underpowered anyway, so who cares. Eventually they freed themselves and split into two separate monster entries.
So, basically the mind flayers somehow conquered an entire race of humans, who were all evil, mind you, and then they bred the entire race into warriors? When your default Intelligence and Wisdom scores both clock in at the high teens, I guess I assumed that it granted you a considerable degree of reason and foresight, both things that this line of action seems to lack.
Moving on, the githzerai decided to move to Limbo/The Elemental Chaos, where they all live in fortress monasteries, again, for some reason. They also abide by rules and schedules strict enough to frustrate a modron. They hate githyanki and mind flayers so much that they build monasteries in the Prime Material/natural world to stage raids against both (the former of which also builds fortresses in the Prime Material/natural world).
Why? Why are they still fighting? What does either side have to gain from this? This is not a "rich" history. It just feels flat and forced, like they are constantly going well out of their to fight each other--I imagine interplanar portals are not cheap to make or maintain--just because. They are literally worlds apart, and they still cannot move past this? Do they not have better things to do or worry about?
Githyanki are not any better. They moved to the Astral Plane/Astral Sea again, which might be more inhospitable than Limbo/The Elemental Chaos, somehow made a deal with Tiamat on red dragons, and are still evil because. The bit about silver swords I can actually get behind, maybe, if only because of their association with the Astral Plane/Astral Sea. Mind you, I think it is silly to exclude them from githzerai due to an emphasis on "martial arts", given that in 4th Edition at least monks got a lot of mileage out of weapons.
Really this article just served to bring to the forefront everything wrong with both...races? Should they be separate races? I do not think so. At best I would go with subraces, but I think that they are different enough culturally to make do. Of course, I would also not shunt the majority into alternate dimensions and make them keep fighting each other for no discernible reason. If I really wanted to go that route, I would plop them both on the same plane and give them something to fight for, which should not be hard given that there are plenty of instances in our history where two ideals clash.