Hey Steve,
1. There may be cases where the user wants to make a long string of cuts right next to points. The easiest way to do this is to disable points so that only edges can be cut. And of course, there may be instances where the user only wants to connect or manipulate points. How about, when the topo tool is selected it automatically enables the p/e modes/buttons if they're disabled, and then if the user wants to cut edges or points only, they can enable/disable whichever? By the way, currently if points are disabled and edges enabled, the topo tool doesn't highlight or work on edges when the mouse is on or near a point.
2. This is useful I suppose, more so than not. If the user wanted it to not be usable then they could either group it or layer lock it. I assumed it was supposed to work the other way since fast select doesn't work on elements when outline/points are disabled for that shading mode.
I've been thinking about this for a while now, but I think it would be far more useful if outline/point draw preferences could be set on a per-shape basis (other per-shape preferences would be nice as well, such as showing textures, materials, X-ray, etc). An option in the shape properties could be, "Override default viewing preferences", and when that is enabled then per-shape options could be selectable. Blender has this type of feature. Later if/when panels are implemented, per-shape viewing preferences would be a snap for the user to set.