EDIT: I think what bothers me about the answer though, is going back to the clay golem's "max" advancement. It's 33 HD, yet the CR increase would stop at 31. If it's every 4, what happens at 32 and 33? Nothing? You just taking those two HD for kicks?
The fact is, CR is a completely arbitrary, meaningless number. It's only function is calculating completely arbitrary and only slightly more meaningful XP, and not only does it do a
BAD job of it, but you're not even using it in your game.
In other words, throw CR out the window. Assess what your monsters are capable of and what your creatures are capable of and judge how difficult a given encounter is from there. For example, if a monster is throwing around DC 30 Phantasmal Killers at will, it's probably a difficult challenge for a party lacking Greater Heroism or Death Ward.
A2: Also, if you follow a Dogma that is different, but not opposed, to your deity's.