I cannot give a precise answer because I am not that familiar with the part. However all processor's with interrupts have "interrupt enable" bits or "interrupt mask" bits. The idea of these bits is to allow the programmer to process or ignore different interrupts at different points in a program.
So the raw interrupt status tells you if there is an interrupt pending regardless of the state of the "interrupt enable" or "interrupt mask" bit. The masked interrupt status tells you there is an interrupt only if the "enable" or "mask" bit is in the appropriate state.