Does the AC 3 pre-order collector editions lack content available with the special edition
Solution 1:
I don't believe that you can get access to all the content with a retail package on the consoles, and I would imagine that the extra parts will be released as DLC at a later date.
However, on the PC the Digital Deluxe Edition will include all the 3 missions as well as the MP content.
There is a table on Wikipedia which lists the editions and which things you get, which could be helpful.
http://en.wikipedia.org/wiki/Assassin's_Creed_III#Retail_editions