1) Metaplots change the setting without input from the players. This is bad because it takes agency away from them whenever the metaplot updates.
No. This is wrong. First the players don't have any right to input. The company owns the setting. Second, no agency is taken away since they never had any agency over the company's setting in the first place.
The only time they have input or agency is in their home game and they get to decide which if any metaplot changes happen, so company metaplot changes aren't really relevant. As an example, I run the Forgotten Realms and don't like either the Spellplague or Sundering, so they never happened. I also like King Azoun, so he never died. What the company did had no impact on my home game at all.
2) No. The "fix" to metaplots is to rewind the clock to when the setting first started.
That isn't necessary in every game, though, so it's not some sort of universal issue. For the many who like the changes, there's nothing to rewind.
However, Eberron points out that metaplots aren't good or necessary by not having them and still having all the benefits other settings gain from their metaplots.
And if that's what Eberron points out, Eberron is partially wrong. Metaplots may not be necessary, but they are neither good or bad. They just are.
Eberron cannot fix problems with other settings, because it is not those other settings.
And because they aren't actually problems of the other settings. They're personal issues. Either YOU like it, or YOU don't.
How do you not see that removing a potential problem that other settings have is a problem? New DMs exist and often make mistakes like including DMPCs. The setting not including any potential non-PC heroes lowers the potential of the happening.
That's what advice is for. The solution is not to ruin things for people who aren't making those mistakes and the ones who can and do learn from mistakes(and we all make mistakes). The solution is to give good advice to the DM on how not to make them in the first place. Advice, not changes to the rules or settings.
That's a solution to a problem other worlds have.
This is objectively false. The problem lies 100% with the DM who runs a DMPC. DMPCs are not setting specific.
That's better than the alternative.
Show me your objective proof of that? Because all I've seen from you so far are personal opinions and unsubstantiated claims of "metaplot bad!"
Other times, it's just better.
To you.