Charley Noble & Ron: There Comes Alibama is re the CSS Alabama according to the notes on "Souvenir Album" (Glendale Records) and also in their songbook. Pretty much as you both quoted above. It's actually both shown as "Cape Malay fishermen" and as "Malay fishermen at the Cape of Good Hope." Then, It is a reference to the Alibama's stop at Table Bay under Captain Semmes in 1863.
Keep in mind that the great bulk of their songs are "improved" by Marais. Often he would take a single verse or just a tune and build a whole song around it. It's impossible to distinguish which are which. Certainly the tune and format & most of the words of this song come straight from his very popular "There Comes Oompy Kahly." I'm content to believe that the fishermen just lightly adapted the well-known "Oompy Kahly" when they sighted the Alibama.