There is not much of an affect. A study on on this showed below 5% if I remeber correct. See the thread Solar panel direction East/West vs North for the link to that study as well as data from my own.
MPPT or Maximum Power Point Tracking is just that. Your MPPT will track the max producing string and optimise for it. Any other string migh not be that optimised, but it still produce power. In the morning your East string will be tracked and in the afternoon the West string will be tracked.