Magicka regen outside of combat appears to be unaffected by the Atronach ever since the mundus was buffed in Stonethorn. I thought things felt a bit off on the PTS, but I didn't think much of it — however after playing on live for a while now, my regen out of combat feels substantially lower than it did last patch. Looking at the character screen using the Harven's Extended Stats addon, it would seem that applying the mundus does not affect Idle magicka regen at all.

Without Atronach: With Atronach:
I made a post in the Bug Reports subforum, but felt that this probably affects enough people that it should be posted in General as well.