The Bootleg Myth is Bust: More Etymology Dysology Uncovered
Have you considered the idea that bootleggers were hiding bottles in the boots, just not the ones they had on? Say, they carried boxes of boots pretending to be shoe makers or sellers while there were bottles carefully hidden inside some of those boots? Not just those boots would hide bottles but also the leather would protect the bottles from breaking, pretty much in the same way we now put our bottles into additional paper or plastic bags.
I have just come across your article while trying to confirm the etymology of the term "Bootleg". Thank you for your alternate view; I certainly can't refute the lack of documentary evidence for the conventional view, however I think you are mistaken.
You seem to be interpreting "bootleg" in a literal sense ("... 150 foot pirate with massive galleon boots ..."), whereas I posit that it is only metaphorical, indicating "concealed" and/or "illicit".
One's bootleg was used to conceal weapons, and bootleg flasks (longer and slimmer) did exist and were more practical than hip flasks that could be crushed by a rider.
I don't think anyone proposes that bootlegs were used to conceal merchantable quantities of liquor any more than the "underworld" was considered to be the literal location of criminals.