That's a fair point.
I think so far as the 1990s are concerned, the problem was that there were rather terrible creators though, and the editor should have been a bit firmer with what they were allowed to get away with and who was allowed to work on the prog at all.
It's hard to believe that with all the creators out there at the time, the editor couldn't find better material. Even if those 1990s creators had the ultimate say on what they would or would not do as far as complying with the editor's requests about changes to their submissions, the editor still had the power to disinclude their stories from the magazine.
You might think a situation where creator-ownership was understood might result in anarchy, but realize that economic necessity is driving those creators to attempt to keep the editor happy, so that the editor will continue to purchase stories from that same creator. Anyone who developed a reputation as "difficult to work with" or a "prima donna" is going to have a short career in the industry.
The other thing to consider is that the editor rarely has those sort of checks & balances overriding his policies and decisions, unless it's a large enough problem to work its way up the corporate chain, to where the editor's reputation for playing hardball with creators is turning talent away from the magazine.
On balance, the publisher will support the editor's decisions. But we've all read the crazy stories of IPC sub-editors who arbitrarily established nutty policies like "there will be an explosion in the third panel of
every page, bar none" (an actual anecdote from TPO), or something as easily irrational. That's because once given the position, there's
no one to tell the editor he can't do something, as long as he isn't spending all the company's budget or something that's getting the CEO's attention.
Freelance creators, even if they are creator-owners of properties, still need to depend on someone to pay them to publish their material, unless they want to undertake the financial risk of publishing it themselves. They can't be so stubborn as to alienate everyone who might want to pay them for doing what they do. They can't expect editors to refrain from having any say about the work they're buying, and they can't afford to be thin-skinned when it comes to criticism.
Some creators have been working in the industry longer than their editors, and there's a good chance they might know what they're talking about when they disagree with an editor. There's always a chance that the editor's right, and the creator's wrong, but does the editor feel strongly enough about his position to be willing to pass on the story altogether (knowing it's going to create a headache for him to fill those pages now)? Likewise, does the creator feel strongly enough about the rightness of his points of contention that he's willing to pass on a paycheck from the magazine? Not all the advantage is on either side.