The short answer is the Vikings' opponents are a little better at covering slot receivers like Thielen than deep threats like Jefferson.
The long answer is, that our advanced matchup ratings give each team a rating against a handful of different play types. For receiving we separate short/deep and left/middle/right. So a team with good linebackers but weak safeties might have a better rating against short passes than they do against deep passes. A player's rating is a weighted average of those based on their own statistics for how their targets are distributed. Strength of schedule, in turn, is the average of matchup ratings.