If there is a rift between Iraqi Al Qaeda and the rest it'll be for the same reason Zarqawi stopped following orders from central... Iraqi Al Qaeda can finance, arm, train, and recruit all on its own while the command in Pashtunistan is distant. The fact tha Iran has since the Syrian War cracked down on AQ transit through Persia has inevitably cut the International Salafi network in half, thereby allowing Iraqi AQ to draw up its own plans.
In intel and Jihadi circles there are rumors that whenever an AQ head like Zarqawi or OBL are caught or killed, it is often by intelligence provided to the enemy by Zawahiri and his loyalists. He has his fingers on the personal data, courier programs, and financial means of every leading AQ figure.
Baghdadi appears to be trying to cut out a Mashriqi Emirate, and he wants all the Euphrates under his writ. This has support from pan-Islamists, but defies the powerful locals, tribes etc and risks seeing AQ evicted. Zawahiri is too wise and experienced to allow this. It's critical that each of AQ's statelets are so firmly rooted that when they declare a union there is no possibility of indigenous mafia banding together to close their shariah courts and attempt disarming their Salafi fighters. Baghdadi must know that he hasn't consolidated Anbar, Diyala, or any part of Sunni Iraq save the countryside and a few neighborhoods in cities like Mosul. He must think that the profits and arms he can pull in al Sham will give him the power to eclipse the Sahwa at home.