Anyone else can't use atlas skills after defeating Arbiter of Divinity?

Am I missing something? I beat the Arbiter of Divinity, and I can't allocate atlas points past that lock. Game also claims in Site of the Chosen that I "am not worthy" despite beating him...Man that was a lot of work for nothing if this is a bug!

Similarly, there is no runestone on Act 4 that I missed, but it keeps claiming I have and some runes can't be unlocked. Does this mysterious runestone exist?

For the runestones in Act 4, you have to grab the 4 torn maps and go to plunder point and complete the expedition there.