Nothing to be confused about. Let's take 2 scenarios involving Jolly Weavile, Jolteon and, say, Heatran.
Jolteon uses Charge Beam, kills something and gets its SpA boosted by 1 stage. Weavile comes in. Let's assume the Weavile is Jolly (Hits 383 Spe).
Scenario 1: Jolteon is Modest, thus, has 359 Spd. Weavile uses Pursuit. Jolteon survives the hit (CB Pursuit does 51.8% - 61%) and Baton Passes to Heatran, who receives the boost unscathed.
Scenario 2: Jolteon is Timid (394 Spd). Jolteon is faster than Weavile, so it Baton Passes the boost to Heatran, who gets hit by Pursuit and shrugs off the NVE 40BP (unboosted) move.
This is the normal in-game behaviour. Shoddy behaves the same.
edit: ninja'd by 2 people