For those of us who don't have a performance per song (lots and lots of work to maintain), but rather have banks of tones that are used generically across many songs, it is nice to have an effect or two that are optional within a given song.
The problem then becomes, you get to the song, select your general performance, and turn on a chorus (for example), but within the song there is another rig you need so you switch over to that rig. When you return to the original rig, your chorus is off now.
I think of it as having one set of switches to control the amp channel (profile) and another set of switches to control the FX presets. This is how a basic multi-channel amp works with a basic MultiFX unit. When you change the amp channel, the FX setting doesn't change, and vice versa.