It's probably just aesthetic. This type of poetic apostrophe doesn't tell you which syllable is stressed and which is not. The only reason we know to pronounce her name with the stress on the Zel is because of the voice acting. Putting an apostrophe in the middle of the name just makes it look more alien and less human.
That must be it. In the game, we just happened to visit a place where we were able to speak with many Githyanki. I paid special attention to the apostrophed words. Although apostrophes were liberally applied to untranslated words in the subtitles, I did not hear any effect. So yes, it is likely to be a silly adornment without any linguistic meaning, something like the heavy metal umlaut. A pity. I hoped there would be more to it.
