i think you're only meant to get to it by falling out of the world in several areas, which becomes a lot more accessible after you get some mobility.
also, where is the first homunculus fight? i don't remember encountering like that on my playthrough.
Viewing post in Crypt Underworld: The End of History comments
Well, if you fall off of the Labyrinth and land on the lakes down below, you'll find a door that leads to a place called... the Sunken Court or Drowned Court, something like that. It seems to be an area where many masked homunculi live, they even have many popes to worship, and in one of the last rooms, you can find it, past the area with the craddle. At least, that's how I think it was called - I didn't get to fight it when I opened its sarchophagus, as I was thrusted out of bounds immediatly. Sadly, you can't repeat the fight either, so I hope I didn't miss any crazy items or so.