It is probably a better idea to look at each case individually before buffing all damage numbers to those of Acheron.
You'd be making a similar argument as the one a lot of people make to defend normal swords being weaker than typed swords "because normal swords have always been weaker than typed swords that's how it must be". Note: I agree with you that that argument makes no sense, I also think that dread venom striker straight up outclasses flourishes, but I digress. To explain, if the Amputator's damage is off compared to status-brandishes, then that is where the problem is situated and you could elevate it to combuster's damage. But then its damage is no longer equal to CIV, so you cannot just say that CIV also has to be on that level or Levi on the level of Acheron, since they have been around for much longer. That said, you might be right that the Amputator's weird spot kind of proves the devs didn't really know what to do with it and that they probably should have done what you said, which is putting Amputator on the level of CIV and CIV/Levi on the level of brandishes/acheron. That would mean nerfing brandishes or buffing CIV/Levi. I think they didn't want to mess with that because buffing CIV/Levi to Acheron damage is scary, it would set the trend to buff all the other swords as well and then they'd simply have to scale up the difficulty to compensate. The other one is even scarier, because nerfing brandishes (or any piece of gear for that matter) is very very risky when a huge part of the playerbase has invested in them and many rely on their brandishes. If you take that away they will feel cheated and surely some will quit. So they went the safe route and added a normal brandish because players wanted it, but made it underpowered so it doesn't impact the game.
I definitely agree with you that it makes no sense normal weapons are supposed to be weaker. The only edge that specialised weapons have or at least should have is their ability to hit slightly harder on 1/3 of the enemies in game, equally hard on 1/3 of the enemies in the game, at the cost of not hitting hard on the last 1/3 of enemies. This can be compensated for by equipping 2 damage types, allowing the player to hit slightly harder on all monsters. And in fact many levels you can already hit for at least normal damage with just 1 specialised weapon. So yes, Amputators damage should be equal to Combusters damage on fiends.
Though like I mentioned earlier, before buffing anything I think it makes sense to look at each case individually. We do not want to buff swords to Acheron level because that is setting a dangerous trend and reverting buffs will never sit well with the community when they have invested time and money crafting a weapon before the nerf.