Well, look at the full context again.
The githzerai are a race of inhabitants of limbo, co-existing with the slaadi, roaming the Prime Material Plane like the githyanki and constantly at war with the latter race.
So, they are constantly at war with the Githyanki, NOT the slaadi with whom the co-exist.
In addition, co-exist usually carries the connotation of mutual tolerance; you don't normally say that you co-exist with someone you are at war with.
Finally, compare the specific, and different, description here:
The githzerai and the mind flayers hold to an uneasy truce, but this is constantly being broken in isolated skirmishes.
See, that's a truce with skirmishes; not co-existence. You can also contrast that with Kuo Toa, who always attack githzerai. (P. 59).
Then, note the Slaadi description-
The slaadi are great frog-like beings, who dwell on the outer plane of Limbo where also dwell the githzerai (q.v.).
Does it say that they are hostile? At war? An uneasy truce? Nope. Just that they both live there.
Again, people can, and did, do what they want. But there isn't any source to say that they were warring with each other when they were introduced.
The integrity actually started stronger; there was usually a distinction between named beings (pantheons of Deities, ahem) and the denizens of the plane. The common denizens of the plane were the alignment of the outer plane. I'm sure there is an exception in 1e (there always is!) but I can't think of it now.
So that's why it makes perfect sense that Githzerai would be coded as CN if they were inhabitants of Limbo.