Note that you get the 'automatic' rewards AFTER the a side mission is resolved (as specified in the cards). If the rebels pick a different side mission, you won't have the reward yet in that mission.

(Also, rebels always have two side missions from the side mission deck to choose from, in addition to possible agenda side missions, so the example is a little off, although you get the meaning.)

The Imperial Player can also buy one agenda side mission when a story mission is coming next, then buy another agenda side mission after the story mission. This is the more probable way to get the rebels need to choose between two side missions and two agenda side missions, guaranteeing at least one reward automatically.