I believe these two statements are incongruous:

Whenever I sing the pro Santi version I usually say a few words about how this version was sung by British seamen with an axe to grind against the Yanks who had whooped our asses quite recently and how many found themselves in the Mexican Army as soldiers of fortune, and so were biased against those upstart colonials.

The fact that so many singers of shanties have no idea of what they are singing about, and worse, that they try to rationalise the old words with new meanings and going so far as to actually change the words to suit their own ideas is rather depressing.

The first statement is just some speculation that appeared in Hugill's book to rationalize the historical inaccuracy of the lyric.

Interestingly, the first comment made on the lyrics of "Santiana," voiced when these songs were still being sung, was:

It may be assumed that the predominance of Santa Anna's name in sailor songs is due to the Southern negroes, who still sing songs of which the name of the Mexican general is the burden. We may therefore class the "Plains of Mexico" with those sailor songs which are of African descent. (Alden 1882)

Alden certainly may have been wrong in his assumption, but I think it counts for something that he was a contemporary, and therefore his sense of the song's cultural connotations carries some weight. This, too, was at a time when an Anglo-American would not be inclined to give "credit" to African-Americans--unless it seemed obvious that this was the case.