I had a thought last night that it may not be necessary to mill polygons at all. Just test that the connectors are already isolated and then ignore the vertices from the brd file.
seemingly there is no difference in the rendering within CP of a board with/without the polygon apart from the connectors (minimal thought/testing on this - here be dragons...).
with polygon

without polygon

suggestion:
if this logic is correct, give people the option via a checkbox not to mill polygon vertices and connectors (if they are already in the milling pattern).
I had a thought last night that it may not be necessary to mill polygons at all. Just test that the connectors are already isolated and then ignore the vertices from the brd file.
seemingly there is no difference in the rendering within CP of a board with/without the polygon apart from the connectors (minimal thought/testing on this - here be dragons...).
with polygon

without polygon

suggestion:
if this logic is correct, give people the option via a checkbox not to mill polygon vertices and connectors (if they are already in the milling pattern).