If I make a one sided board, I select "generate top xxxx".
Especially for "milling" - in the sense of "cutting the board outline" or "cutting a hole" - seems to be sufficient to do it from one side, e.g the top side of the board.
So why do you generate top and bottom mill-files?
Even on a twosided board holes and the circumference are cutting through the board and one mill file will be enough.
Moving the checkbox from the "Board" pane to two checkboxes in the "Top Side" and "Bottom Side" pane, respectively, will do the trick easily.

Just an idea...
Harald