You keep using the term "rate", while using a raw number (5). The only way you can fairly/accurately apply "five penalties per season" as a "rate" when comparing JW to the rest of the team is if you take those other players' penalties per snap and interpolate it out using JW's number of snaps (1100, which includes 84 ST snaps).
Witten incurs .0045 penalties per play that he plays (5 penalties over 1100 snaps)...that's his "rate". If you apply the same formula to all other players to come up with their rate, then you'd have a fair comparison when comparing them to Witten.
Simply assigning every player 5 penalties per year regardless of the number of snaps played and is meaningless. For example, OScan had four penalties in 672 snaps ( .006 penalties/snap) At that rate, if he had played 1100 snaps, he would have incurred 6.6 penalties for the year. Mayowa had four penalties in 386 snaps
(.0103 penalties/snap) At that rate, he would have committed 14.3 penalties for the year had he played 1100 snaps.
Yes, Witten commits penalties, but his penalties are not killing the team. About half the team commits penalties at a higher rate than him.