Here is the fundamental problem with 538's analysis:
They base their analysis primarily off of each team's ELO ratings, similar to how chess players are ranked. BUT, the problem is, they generate those ELO ratings using more than just this year's data. It is actually a running total going back to when the franchises were founded.
Tennessee and Jacksonville are each punished heavily for being so bad prior to this year. For example, 11-7 Atlanta is ranked almost 100 points ahead of 12-6 Jacksonville. Does that make sense? Also ranked ahead of Jacksonville are three 9-7 teams: Dallas, LA Chargers and Seattle.
So yes, according to 538, the Chargers are a tougher opponent than the Jaguars. Sorry if I have a hard time taking such an analysis terribly seriously.