So I started two more campaigns of IA recently as the Imperials (only been a rebel before) and by chance in one of them I had enough influence to after game three to play an Agenda Side mission. While debating it I didn't like that it was a risk to use the mission since the Rebels had a chance to deny my investment of influence. I like to get max impact out of my resources so anything that's not or doesn't provide a permanent bonus is not to my play style. And the wording kept bothering me, "After the Rebels resolve any other side mission, discard and claim reward" or whatever it specifically says. Which gave me an interesting thought. Can I save up and hope to draw two agenda side missions, buy/play both, auto win the second one of them after they try to stop me in the first, or whatever order? Could that have been the intent?

I do not see any problems with this. However you will be hoarding influence for a relatively long time.

Sneaky. I like it.

However, I believe the Imperial Missions state that you only score them automatically if the Rebels run one their own missions instead of yours, so that second mission you bought would remain active until the next side mission phase.

I do not see any problems with this. However you will be hoarding influence for a relatively long time.

Not just hoarding for a while, but hoarding until you managed to flip 2 out of the 4 or 5 agenda cards you flip. Any unchosen agenda cards are shuffled back in.