i did a google search for "waypoint graph generation"
this was the first hit:
http://www.gamedev.net/page/resources/_/technical/artificial-intelligence/navigation-graph-generation-r2805
while talking about hierarchical waypoint graphs, it says:
"Indeed, first we can identify the super-node corresponding to the region where the agent is located and the super-node for the destination region. An A* run on super graph can return either "no path" if the regions are not connected, or a navigable path in super graph. This path consists of a list of regions the agent needs to visit in order to reach its destination. Navigation within each region is handled by a-star on regular graph."
in my case, the set of collision maps that lie in line of sight from start to goal would be the list of regions to visit. there is no special connectivity. its just a 2d array[500][500] of map squares, and each map square has an array[88][88] of collision maps, and each collision map is an array[300][300] in size, at a resolution of 1 unit = 1 foot. about the only thing special is oceans. in that case, a search of the far edge of an area for an appropriate goal node would fail, as all nodes in the adjacent chunk are impassable.
which means i'm back to my original chunking algo of: A* across a chunk to the next chunk, and repeat, for each chunk along the line from original start to ultimate goal.
whether i use A* on a grid map, use a nav mesh, or a waypoint map.