It looks like you have a decent gap when the screen is on. I would most likely get like a .25 square dowel piece of wood and cut it to fit on the bottom section there. This will leave a clean edge on the bottom. You defintelly cannot square off those areas with glazing putty. Yes I know, you have to use bondo. Fact is glazing putty is just for small surface imperfections. You will need some filler in order to build out those sections. To get a squre corner, take a square block and wrap some sand paper around it. Use this in the edges to create that shape.
BTW, you can get a wood dowel at home depot, they are like 36'' long and cost like 0.70 cents.