This started happening within the last couple of months. Whenever I open a new tab in Safari, my custom BTT toolbar is replaced by the standard system one. I can hit the close "x" on the far left of the bar to close it and return to my custom one, but I have to do it each time.
Touch Bar MacBook Pro 2016
High Sierra 10.13.5
Latest Alpha version of BTT (has existed for many versions)
Unfortunately the Safari Touch Bar takes precedence over the BTT Touch Bar. I currently don't think this can be fixed given the available API 
Okay, but it used to not do this.... do you think something changed on the OS side? Just want to make sure it wasn't an unintended side-effect of another change...
Yep, unfortunately there was a change in Safari which now shows the favorites in a modal Touch Bar