Just a small nugget of info:
Oda has made an end of Jump (WSJ #50) comment. My interpertation of this or the gist of this from reading around is, that there was some general unhappiness/opposition to the mangji symbol 卍 (obviously which is generally assosiated with the Nazi party's swastika) being used in the original flag design.
So from my understanding the manga version, has been changed to the skull & crossbones anime version. I assume the changed ver. appears in Ch.434, and Oda has made this comment to clear any confusion.