Because Phil hasn't given up on XBone. If and when they gain significant market share and become too big to be ignored, then the parity clause will be awesome for them, because it means developers will have no real choice but to delay their PS4 games. If they don't have the resources to develop two versions of their games simultaneously, then that's even better for MS, because now that game becomes an XBox exclusive for a period of time.
It's like the DRM stuff. There's no reason to give it up unless it prevents people from buying the hardware. If people are buying the hardware, then the clause needs to stay, because the larger their install base, the more effective the clause becomes.
Granting exceptions allows them to demonstrate how generous and reasonable they are. Plus, it lets them get the "big" games on to their platform as needed.
This particular parity clause is launch parity. Basically, if your game comes to PlayStation first, then it's not welcome on XBox, ever. Simultaneous launches are permitted if you have the resources to deliver them, but if not, then you need to release on XBox first.
Devs are also held to feature parity, meaning if some feature is present on the PS version of your game, then you need to have the same feature on the XB version. If you can't have that feature on XB either because it's technically infeasible or MS simply don't allow it then you need to get Microsoft's permission before you can include it on the PlayStation version. As mentioned above, sometimes MS are generous enough to allow it, but if not, that extra development effort you put in to the PS version goes right down the drain.
I think feature parity is actually the more harmful clause since it doesn't merely delay games, but actively stifles innovation in the industry but for whatever reason, launch parity is the one that gets all the press.