Hi, I run most of the major mods that you do except mine run on top of GWX.
I always thought the Merchant fleet mod had very few flying flags, but most ships have the flags painted on the hull. The stock ships and others I presume have the standard flying flag.
I could be wrong though as I haven't played for a few months.
Is that mods soup you published loaded in the order you displayed? its a little different to mine.
Cheers Graeme