Here is a version. In order to do the boolean subtract, found it necessary to
extrude the red circles by 0.2 mm (or units), then do the flow on to the cylinder.

Select the red circles, using style color, and do extrude of 0.2 mm, with checkbox of BOTH directions.
Select the red extrusions, hit flow, then select the planar rectangle, then the cylinder. Flow occurs after several seconds.

Select the cylinder, and all the red and rectangular regions, but not the red extruded circles on the cylinder. Invert selection
and change the color of those red extruded circles on the cylinder to green.

Next do the boolean subtract of the cylinder with the green extruded circles.




Maybe this is not exactly what you wanted... Or the easiest way...