Your understanding is correct, however, if your workflow is interrupted and you need the table for cutting (say, if you ruined a part), you can switch to cutting with the incra removed, and resume your routing with it reinstalled, no set up necessary.
If you have 1 or 2 common bits you work with constantly, you can dedicate one of the scales to that bit. 1/4” and 1/2” plywood bits might be an example if you build a lot of cabinets or rabbeted drawers.
If you’re doing an operating that requires two bits (sliding dovetail or T slot), you can hog out your groove, remove the fence if it’s in the way, swap to your dovetail or T slot bit, put the fence back and just adjust the height. But usually you have enough room to slide the fence back without needing to remove the whole fence.
It’s just an added convenience that can save some time and give you more consistent results.
As for the positioner being square to the table. If you use the miter slot on the table or a sliding table on the CMS, you’ll need it square. With the incra, you set it up square once, and you’re done. No need to re-square after the fence goes off and on again. Again, a time saving convenience.