I "love" double stadard where we justify the bastion being off-limits for the dm by toxic dm behavior and that is apparently fine, but being wary of this very rule being abused by toxic players is either "made up hypothetical" or fault of individuals that cannot be used to justify general attitude towards something.
The only people talking about "toxic" DMs are you and Micah Sweet. Everyone else is talking about DMs doing regular DM things: if the Bastions are not singled-out as being controlled by players, than many (if not most) DMs will naturally see them as something they (the DMs) control, and
with the best of intentions use them to complicate the PCs' lives.
To be clear, there is nothing wrong with that concept! It is how it's worked in D&D since 1974. Like anything in the game, over the years it's been done well, and done badly.
But the idea of Bastions, specifically, is to give players a piece of the world that
they control as an extension of their characters. That they can--for the most part and
within the confines of the kind of world that the DM has created--design and flesh out however they see fit, and which won't be involved in the game narrative unless
they want it to be.
Now, I personally don't see it as an issue. It sounds like a fun little mini-game. But if a DM does have an issue with that concept, there are, like, two super easy approaches.
1) Don't use the rules. They're an option available at the DM's discretion.
2) Talk with the players and say, "Hey, I think you guys will have fun with these rules, but I want to use them in the traditional style, where they are ultimately controlled by the DM and can be used in the game narrative as I see fit."
Toxicity has nothing to do with it. Players should not play with toxic DMs, and DMs should not run games for toxic players, period.