Well, I did look at "Flag of Portugal" in Wikipedia. Quite an impressive explanation of the flag, its history, its changes over time. The connection between the armillary sphere, being "an important astronomical and navigational instrument for the Portuguese sailors", and "the most important period of the nation - the Portuguese discoveries -" is well explained. However, when looking for "Portuguese shield", the Internet shows a lot of pictures of the shield alone, without the sphere. This may explain what happened. Given the marketing effort of IWC, stressing the maritime connotation to the Portuguese watch (which we all know is incorrect, the two Portuguese gentlemen contacting IWC in the 20th century only had a nice watch in mind), the sphere should be there.
By the way: when really wanting to correct the mistake, I cannot imagine that a redesign of a medallion would take so much time. It is not like changing a vital part of the movement. If I were IWC, I would not like to have a second Sidney.
Kind regards,
Paul