I had at some point found out Close Hole has options(beyond "Through All Volumes") but it took me a while to figure out how I got that "Tool Options" panel. I found out that enabling the "On Plane" checkbox(next to "Through All Volumes") on the "Cut Off" tool brings this panel up for "Close Hole" but it doesn't have this option flag itself...is this a bug?
It's been useful to change settings as it seems to allow me to not damage other parts of my mesh(environment) accidentally(it would affect triangles considerably further away from the area I selected/brushed...although triangles would often delete themselves(or perhaps visibility was just toggled) on triangles nearby still, even though they're out of the target area.