I finally found this thread again. I just want to document how this issue has continued to haunt me 2+ yeas later:
2021-06 : This is when the issue originally appeared for me, after upgrading to Mojave on my 2017 MBP (as per my old comment on this thread).
2022-01 : I got a new 2021 MBP and fresh installed every single app / manually transferred files. It appeared the issue was resolved.
2023-02 : The issue returned. I actually documented it's resurgence here while trying to troubleshoot what might have been an unrelated issue. I guess this might mean that for those who have this, reformating is only a temporary fix.
I can confirm that Andreas's terminal workaround does stop BTT from popping up, but results in two other more problematic issues:
1.) The current window of whatever app you are running will loose focus whenever the preferences pane would've popped up. This means you may be typing something or interacting with something, and then suddenly loose all input. This is very annoying because without the preferences pane showing, the loss of input can go unnoticed for a few moments.
2.) Shortcuts invoking the BTT preferences will no longer work (I am constantly adding/changing things in BTT and have the preferences mapped to one of my mouse buttons, so it is a significant loss for me).
For me currently the BTT preferences will pop up anywhere from 5-20 times during the course of a 10 hour workday. I can't live without BTT so even if it was happening 200 times per day I would still continue on using BTT without question lol. That said I dream of the day this will cease to be an issue.