Unfortunately there are more variables that need to be considered, including things like product quality and manufacturing yield.
Quality is impacted by component quality (what supply chain do you anticipate - Aliexpress end or Mouser etc?) as well as manufacturing, not to mention the design and shipping losses and customer returns. Yield is impacted by all of those factors as well as the manufacturers capability and interpretation of what you want. Your design can also increase manufacturing costs if you do not DFM "design for manufacturing" and also design to take full advantage of your manufacturers capabilities. Bunny Huang has several good articles about this.
From your question and "low" quantities, it seems that like me you probably have little manufacturing experience, so I recommend you also look top down pricing - compare Aliexpress & Sparkfun etc online retail prices for the Due and imagine 50% or more markup. See this article[/ [url]https://learn.adafruit.com/how-to-build-a-hardware-startup/pricing-your-producturl] (one of many on the web).
Octopart have several good articles on cost of materials versus quantity as well.