I'm not really sure. (I have now attached the pictures of the disassembled carb for you to review.)
In answering your question, I can only say that based upon the picture of the carb I posted (pre disassembly), I would have said the choke cable enters the carb from the bottom of the hollow choke assembly. However, this contradicts your thoughts as well as the Motobecane manual. It doesn't seem logical either because it seems like it would be harder to create tension. However, I swear this is how it was on my ped for a long time. You can see the end of the choke cable right there in the picture on the top of the carb...