Unfortunately I don't know what causes the popups while the BTT settings are closed for some users. It seems like some process tries to start BTT, but I have never figured out which one.
There is a workaround described here: Configuration window appears out of the blue - Bug Reports - BetterTouchTool Community (folivora.ai)
@Frank1 I think you issue is a bit different and can not be prevented completely with BTT's current architecture. For some actions BTT needs to be the "active" app. Thus some actions in BTT will activate the BTT process and this causes any open BTT windows to show.