I use a utility called Magnet to do some window management tasks, like resizing. I believe the way it's able to do this is through the Accessibility features of the OS. TheBrain (at least up to 9.0.215) doesn't respond to Magnet commands, which leads me to believe it doesn't play well with the accessibility features of OS X in general.

The app has a FAQ entry:

Why is my window not resizing?

Magnet can handle all standard resizable windows in OS X for you. Magnet can not do anything with non-standard windows used by some developers. Fortunately, such windows are quite rare. Adobe Creative Suite & Creative Cloud apps older than 2017 version is not supported exactly for this reason.

Which isn't technical at all, but, seems to account for the behaviour.

Just thought I'd share that.
FYI, changes made in 9.0.220 enable Magnet to work with TheBrain.

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