Immortals set them, so there is that. Shokai has hardly been active enough to say how things should work in fort, or that how it worked shall be how it shall always work. I saw him vis I think two times in the 8 years I played, so I wouldn't say he is relevant in any capacity to determining how fort should operate. Now, if the claim is Baer smote Shokai in a violent coup causing Shokai to fade away, maybe that is relevant. I have no idea if that happened though.
Fort works how current fort immortals say it works, same as every cabal. While many give deference to traditional rules, they don't seem to take a hard line stance and allow some flexibility and change to occur. Otherwise everything just gets too damn stale. Mortals interpret rules, but Immortals set the general rules and supposedly keep things from getting to out of line with cabal dogma.
Some players just have a hard time accepting any deviation from their own view of how a cabal works.
There was Destuvius and empire, and who knows how many people bitch any time a new battle imm does anything that Thror didn't explicitly condone15 years ago. And then there is the thing with trib now.
I can't imagine Baer deviated so hard core from the original fort concepts as to morph it into something completely different.
She mostly ignored nexus as rayihn from what I saw, but actually every nexus imm ignored that cabal from what I saw. Except Twist when he booted me.
Sounds more like you personally disagreed with her choices, but that does not mean they were objectively bad ones, or that any alternatives would have been better.
If Baer had a flaw that led to countless other Imms leaving, sure that's a negative, but I am in no position to know if that is true, and I generally don't take the word of a person I've never heard of or have reason to believe. I have no idea what Imm he even claims to have been. Not saying he is wrong or lying, just that I don't have the ability to know his own biases and have seen nothing to actually support his statements, so his opinion is not really all that relevant to me. Just as mine is not to him, or to you.
I know from my player perspective Baer worked to make CF a better place, and was far more engaged than pretty much any other Imm while I played. Maybe not everyone shared her vision for CF, but that does not make her bad. I would guess more players had postive than negative experiences with her on account of her willingingness to actually RP her Imm on a regular and consistent basis. And players often credited bad things to Baer that were not done by her.
Half the grief Baer got was from players who hated players that followed her. I think most players that gave her a shot as a follower found it was a pretty fun experience. That's a net positive to me. And keep in mind, I came to CF when Baer was already an Imm. I only saw with and without baer, it was better to me with. I never knew CF pre Baer.