Trying to keep the actual size viewed from the window is going to be tricky. Overlaying a grid on top of the panel is the only way to do it, I suspect. You'll have to mark what is seen from the window, then remove the grid and add a quarter inch to each side of your markings. Trim each window from the panel including the seam allowance. That will cut out what the frame would ordinarily hide from view in the actual size view. You can see what is not going to be seen from the panel before you cut into the panel.
Make sure the grid is the finished width of the window frames, not the unfinished width. You can cut strips of low quality fabric to do the overlay. Overlay the entire panel before marking so you can see if it going to work the way you want it to.
I'm with you about those elongated images. I find most attic windows done with panels have frames that are way too thick and that tends to distort the image.
You may want to thin the sides of the frame instead to include more of the panel. Then do the overlay again and see what happens.
Another recommendation -- buy a second panel in case you're not happy with the overlay method.
Good luck and be sure to show us pictures!