I noticed there are packages in the 2009 MY (maybe even 2008). The 4Runner did not come with any "packages" from Toyota to at least 2006. The regional distributors order the 4Runners with certain option combinations, which they may call certain groups of options a package. The options were available individually, though some had prerequisites, i.e. rear seat entertainment system (RSES in '06) it has to have the moonroof and JBL sound system to get it; for navigation must have HomeLink.
Leather and third row are not available from Toyota for the Sport Edition.
In my area, SR5 and SEs don't have the JBL or double decker option. Nav are mainly found on V8 Limiteds. Most, if not all 2WD are V6 SR5s only. It's all upto what the regional distributor wants to order.