As far as the overall plot of Final Fantasy XI goes, saying Shadow Lord is the final boss is like saying Edea is the final boss of FFVIII after you defeat her at the end of the second disc. The plot of Rise of the Zilart picks up immediately after you defeat the Shadow Lord. Calling the expansions, specifically Rise of the Zilart and Chains of Promathia, akin to extra content and maxing out one's character indicates a gross misunderstanding of the continuity of Final Fantasy XI's plot. If anything, the originally released plot, Rise of the Zilart, and Chains of Promathia are more akin to The Fellowship of the Ring, The Two Towers and The Return of the King as three parts of the same narrative. Both are those expansions are necessary to even understand what really happened with the Shadow Lord and how he came to be.