You can make a super rare caste (Like, make it 1 and make the most populous caste 100000 or something like that) for Elder Brains and restrict the leadership position of the civilization to that caste. An example of the syntax:
[POSITION:MONARCH]
...
[ALLOWED_CREATURE:CREATURE:CASTE]

So in this case it'd be [ALLOWED_CREATURE:ILLITHID:ELDER_BRAIN] or something like that.

Just an idea, it'd require a lot of body plan work to make an entire body that's just a huge brain with tentacles.

@brenbold

My plan is to make the Elder Brain a building with special reactions, in earlier editions of D&D the Elder Brain was typically less of an Overlord and more of like a repository of information

I was planning to make reactions for stuff like "Commune with the Elder Brain" to get knowledge buffs and such, which I could only really do with a Building

Imo, it's probably more exciting to a generated narrative if the elder brain were a person instead of a building - one that could die, etc. If it were a building, you could just make a bunch of them and they wouldn't be that special. You could have other ithilids commune with the elder brain and gain buffs with a "Greeting" interaction. If you wanted it to be big, you could give it a big 2x3 sprite.

I suppose I could, yes I'd have to look into castes to figure it out. And that's the second opinion that wants the Elder Brain a creature, I just hope they don't show up NORMALLY, but I'll see what I can do

Thanks for the suggestion!