Polygon packing doesn't try all rotations of your images. It tries rotating by 90 degrees to find which packs best. It may be better to draw your blue line straight.
Packing is "NP hard" meaning it can only give a "best effort" solution. While you can pack the 3 images manually, the texture packer may not be able to.
Typically there are many images, so even if a few aren't packed as you would do it manually, it still packs well.