Theories

Mother Horse Eyes is a Flesh Interface

The Investigator's Narrative and the CIA Narrative describe how government agencies investigating the flesh interfaces began to use children in their experiments, owing to their ability to survive "Travel" with relatively few side effects. The ideal age for a subject would therefore be young enough to survive undamaged, but old enough to remember and recount the experience. All of the children who are depicted having encounters with Mother Horse Eyes appear to fall into this age range.

Furthermore, the children are mysteriously taken from their parents by unidentified characters (described as "them" in one account) and delivered to Mother Horse Eyes. This matches the description in the CIA Researcher's Narrative of the abduction process used by the agency to obtain research subjects.

The children are also given some kind of hallucinogenic "medicine" by Mother Horse Eyes that keeps them under her control. This medicine may be the LSD or some other related hallucinogen that the government agencies are described to be experimenting with.

Mother Horse Eyes is depicted as a monstrous assemblage of disintegrating flesh from various separate creatures, much in the same way that flesh interfaces seem to incorporate the flesh of many people. Post 45 of the Mother Horse Eyes Narrative describes how Mother Horse Eyes seems to be reassembled by mysterious flute-like music which matches the description of music on the other side of the Flesh Interfaces reported to the government agency investigators. Another mention of flute music is made in Karen's Narrative, where she describes the 'cheap' soundtrack of the 'Children of the Forest' game as flute-like.

Chitinous Cruciforms are related to the arthropods of The Arthropod's Narrative

Mother and Flesh Interfaces are related to Sarkicism of the SCP Wiki

both of these universes include instances of body modification and horror, and seemingly include an instance of a godlike figure related to corruption like Mother and Yaldabaoth.