What you are forgetting is that bounties are based on what the government has seen. We as an audience know Zoro Post-DR (w/ 320M) could solo a pacifista, so he should have a higher bounty than that and the 320M bounty is inaccurate. But the government can only judge Zoro on what they had seen up until that point, and government determined that Zoro's actions in DR merited a 320M bounty.
So instead of seeing it as an accurate 320M bounty pirate can beat a pacifista (it can't), see it as a accurate 320M bounty pirate being able to beat Pica.
I think this is the same with the captain bounties. The captains tend to be the ones that show their power the most, thus the government has more information to give accurate bounties. This makes the captains bounties a lot higher, but a lot more accurate to their power/influence. On the other hand, the less a subordinate is in the public eye (the less they show how dangerous they are), the more the government will underestimate their threat level. Giving them an inaccurate bounty that is too low to what we know of their true threat from an audience's perspective and judge them based on the threat level of their captain. This is why the post-DR bounties for most strawhats was +50M and the post-Wano was +300M. Only cases where these standard bounty raises don't happen are cases like when subordinates take out the highest ranking members of a rival pirate crew (Zoro beating Pica -> +200M, Zoro beating King -> +791M, Sanji beating Queen -> +702M), or rumors/infamy (Usopp being called a massive threat by Doffy in DR -> +170M, Buggy being considered a great uniter of strong underlings -> +3.174B).
Also note, cases were governments give bounties with false information to the public to make them wanted but hide their true threat. Example is Robin knowing how to read poneglyphs, so the government wants her captured but they can't say she can read poneglyphs so they put out the false claim she took down battleships for the 79M bounty. In fact, I think now her bounty is more in line with her actual threat to the government.
Points that make this not make sense:
- Luffy, Zoro and Sanji soloed pacifistas when returning to Sabaody and their bounty was not updated. But this could be due to those models not being as strong as they used to be and the government didn't see merit in raising their bounties. (But I really think this is an oversight by Oda and their bounties should have gone up for that)
- Jinbei going +1B when he defeated a member of the Tobi Roppo like Franky/Robin. But it could be because of Jinbei's infamy and now joining Luffy and having his captain's infamy influence his bounty.
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