Dr. Livesey is The Doctor HimselfWell, if he was Merlin, this can't be too far a stretch.
Long John Silver's pirates are secretly Patriots agents traveled back in timethey sent back in time to Captain flint's treasure, and the Patriots ordered them to kill John Silver if he helped out Captain Smollet
Alternatley, Long John Silver's pirates are secretly collaborated with the The East India Trading Co.
Long John Silver eventually invested his share of the treasure to open a seafood restaurantObviously, it became huge later on. You may have even eaten there.