Namely here, a definition of 含む 「三省堂」:
〈五〉 内部｛ないぶ｝に‐入｛い｝れておく（つつみもつ）． (派)(～)み
My intuition suggests it could stress the class of 'inside things' to make it more abstract (putting inside anything as opposed to restricted physical space), but my intuition has been wrong many, many times before.
I've found two other examples:
［持続］： 〈スル〉 長く‐続く（保ち続ける）こと
「生える」： 〈下〉 植物が-芽を出す（生長する）． ∥ 歯がのびて出る．
Perhaps it's used to illustrate things? E.g. 生える doesn't have to refer to sprouting plants but the concrete analogy makes the meaning so much clearer. I could be totally wrong, however.
Well, turns out I was wrong!