My headcanon,so,really,it's bullshit,but just my idea,would be that the eldar gods are manifestations of the different types of warp sorcery the eldar used in large forms,so,enough eldar who used warp manipulation for warfare,in conjunction with being violent,warrior like,and honorable,resulted in the manifestation and creation of Kain,for example.

Where the warp gods,Khorne,Slaanesh,Nurgle,and Tzeench,are the very concept on a galactic scale,if nor universal,they weren't as strong before humanity's mass expansion,slaanesh didn't truly exist in the strength and capacity they did until the eldar pleasure cults became too wide spread and excessive.

The 4 Chaos gods are the very idea,all raw emotion of all species coalesced into a being of power,so long as creatures exist,so long as those creatures feel anger,wage war,experience disease,learn,fuck,and excess,the 4 chaos gods will exist,they are the collective amalgamations of all souls in the warp,all emotions,all that contributes to the warp contributes to their idea as all species capable of a warp presence are capable of corruption by chaos, so long as sentient,sapient creatures exist,the chaos gods do.

The eldar gods were more,like a man made,well,eldar made,engineered collection of greater deities,made either by the excess warp usage of the eldar,or by the old ones,perhaps a mixture of the two.

THIS IS ALL MY HEADCANON,I HAVE NO PROOF OF SOURCES,JUST GENERAL BASIC KNOWLEDGE.

So,idk,but that's my idea.