I tend to think of enemies and bosses top down, usually coming up with a child deformity, demon or other abomination and designing around how it looks.
with items though its def. a bottom up design. i always think up the effect 1st then design the item around what it does, because its usually more important to the games design than an enemy or boss.
and yes, a stone baby was something i played with in isaac, the stone heads were going to be stone babies but they just looked weird…