in order to get a good cutout u have to experiment by rotating your object, set it to align with your wall,
and edit it Manuel ,even 0.1 deg up or down can give u a good cutout

Example ;
1 If your wall has a Angle of 120 deg, set the angle of the window to 338.5 or 158.4

2 If your wall has a Angle of -103 deg, set the angle of the window to 192.9 or 12.8