Just updated BetterTouchTool to V2.645, finding that the accessibility permission popup cannot be dismissed. The close icon at the right corner of the popup panel is just missing. Luckily, BTT can work well for touch/click functions without those accessibility permissions.
After some searching around, one github issue comment has the way to diable the popup:
defaults write com.hegenberg.BetterTouchTool BTTDisableAcccessibilityCheck YES
Update: It’s only valid for High Sierra and previous OS X versions. Mojave will require enabling accessibility for BTT.