Luffy commands people under him. His influence increased after dressrosa with the introduction of grand fleet. even if he beat a yc1. his bounty shouldn't have easily crossed 1 B.
It's overall thing and considering how harmful he is to the WG. Not just combact ability.
and Zoro getting 1.1 B is still joke to me. He is easily 1.6-2.2 B character. surpassing boa and crocodile.
and crocodile due to his influece got 1.9 B.
So influence and harmful idea agaisnt the WG do put up a bounty for you.
zoro was a pirate hunter not a marine hunter. WG has no reaosn to fear zoro except his a powerhouse for strawhat.
his bounty is purely his combact skills. unlike luffy.