Hmm, just was made aware of Monsters of the Multiverse that changed this up.
Basically, bg3 seems at present to be working from Tome of Foes, but I would not be surprised if they altered things to be in line with Monsters of the Multiverse.
Yes, Monsters of the Multiverse changed a lot of the player races that got published in Volo's Guide and Tome of Foes. If you haven't managed to look at that book yet, you can look
here and use the list to compare, because it has entries for the races from different sources.
The biggest change to Githyanki was that you can now change your extra proficiencies on long rest if you want to. Larian are still using the MTof version at the moment, and i don't think that will change because of the odd engine behavior around choosing extra skill proficiencies that they seem to have.