I use the mute tool for comping all the time, and it doesn't seem to get me in much trouble,
I remember I used 'rebuild layers' several times comping a guitar track last week without causing a problem,
so I had a play with Sonar 8.0.1 to see if I could make it do what you described above.
I was not able to cause any problem by moving clips between layers, or using 'rebuild layers' 'show layers' or 'remove empty layers'
I was able to cause the problem where you loose comp info by deleting a layer, but I noticed that that only occurs when the layer you delete overlaps other layers that have been comped, so it is possible to work around by dragging or slipping the layer you want to delete until it doesn't overlap anything.
Less than ideal I agree, but not unusable...