It seems like right now planner makes blueprints with just quality modules. In practice the math is a bit more complicated - adding productivity modules, if supported by the recipe can make the whole cycle more efficient. Made more complex by having to support modded quality tiers and modded modules :)
For the moment all the machines get quality modules except the last one who gets productivity modules if supported (there is also a selector option where you can define if last machine gets productivity/speed/efficiency modules)
I have made an analysis about that, it can be implemented but I need to think about an UI to make it user friendly