I'm having this same issue, and I posted about it in the GoldenChaos-BTT thread. No matter what I do, the default "x" and MacOS control strip come back as soon as I navigate away from the "General Touch Bar Settings" window.
- Type of Mac: Macbook Pro 15" 2016
- macOS version: 10.14.1
- BetterTouchTool version: 2.645 (954)