Bounty was released along side with Infiltrate. There are currently no Imperial units with Infiltrate, on release there was only 1 unit with Bounty whilst rebels had 2 with Infiltrate. Additionally, you can have multiple units with infiltrate in an army list where an imperial could only have 1. Now 2 with Bossk.
For Recover Supplies, its quite easy for Rebels to Infiltrate and run away with the middle box. Bounty provides an additional means for imperials to even the score if this happens.
For Key Positions, you have options to infiltrate the back line objective (most of the time there is only 1 unit here holding it). The Imperial player has to focus additional resources to deal with it, therefore less units trying to claim the middle. Or can try go for the bounty.
For Intercept Transmissions, you can claim the middle earlier for quick points, or disrupt the back line with Infiltrate. Bounty can give options to even the score.
For Breakthrough you can literally infiltrate into a weakly defended area of their deployment zone. Once again bounty can give options to even the score somewhat.
For Moisture Vaporators not much you can do here, but theres not much a bounty hunter can do as well unless the rebel player makes a mistake.
For all situations an infiltrating unit can deploy to intercept the bounty hunter.
Not saying that the above is right and yes i know most people don't use units with Infiltrate anymore. I'm just saying that this is probably what the designers were thinking when they introduced Bounty and Infiltrate. FFG systems have a tradition of keeping factions asymmetrical, or 'same same but different'.