I’ve been running well of skelos and the final boss is not spawning
Unfortunately, I believe that has been a bug for a while. (Years) There are a few workarounds people have used if you search on the old interwebs.
You either speed run towards him in less than 3 min or he will be gone.
The second workaround is, when you reach his throne, you turn left, get away as far as you can, fight a group of snakeman mobs and loot the chests, then you come back, he will be there again.