OK, got you about the Window is upside-down and inverted.
@yorik is the main developer of the Arch / BIM workbench, he should be the one know in details what's happening - seem he's extremely busy recent weeks so may need some patient.
In the meantime, just as @yorik had mentioned can do it manually - just create the window 'in the air', then turn on it base sketch, and move and rotate the sketch to the wall position as desired. In the window's Host attirbute to choose the Wall object. Recompute and it should be done. There are a number of discussion how to place a window in the forum.