What factors should be considered when calculating the true cost to produce an item?
For example. Does one need to consider how much it cost to extract the resource, then to process it and then then to make the actual end product?
Lastly, how close (assuming this is the case) does the product overview in the WIKI actually reflect the Production Cost? 
To calculate the cost of manufacturing, you do indeed need to include the cost of the resources.
If I want to figure out what my coffee is costing me to make, I have to add up:
If I'm purchasing any of my materials from the market, then I pick an average for what I normally pay. That about covers it as far as determining things like what price you can pay for materials or what price you can charge on the market and still make a reasonable profit.
Now, if you want to dig a little deeper, I like to divide profit by the number of buildings it takes to manufacture it. That way I can tell which products will net me the best 'profit per plot'. It doesn't take long before those 100 map spots are filled. Some products can look really attractive only until you do those figures.
I can't answer about the wiki - I recently returned after losing my hard drive and all the IT records and spreadsheets I had on it (groan), so I'm starting from scratch again.
Not your true costs, but a overview:
production costs in the wiki
If you ask me it did be the total amount of profit gain per space used, and the consumption of a particular resource. Since 100 space seems to be the true limitation after about a week into this game, I did suggest total profit/space consumption.
