After some tests I came to the conclusion that Cart Packed with Gold blocks Custodian's respawn.
I don't really know how or why but while the cart is alive Custodian simply doesn't respawn. Killing Custodian then killing the cart works like a charm. Depending on how many people are online in the world Custodian will respawn between 4 to 10 minutes.
With that said, it is likely possible to purposely block the boss spawn by killing and leaving the spot without going through the flames where the cart is. In this scenario you need to wait and be lucky that a cobra walks south and ends up killing the cart.