First off, please let me extend my thanks for this passion project. This tool is so powerful and so versatile that I've been able to take a touch bar that was essentially forced on me and turn it into a productivity boon. Every article and post I found on how to take control of the touch bar pointed me to BTT. I purchased a lifetime license two days into my 45 day trial.
I just filed a couple of touch bar bugs (Opt Hides "Hide on Cmd" Button, 3-State Touch Bar Workaround). Isolating these behaviors from a complicated toolbar I'm building required taking a big step back and starting from scratch with the most basic use cases. Given all the options for modifier keys, keyboard shortcuts, and triggers displaying entire toolbars, I realized it gets real easy to hang yourself. It's really a testament to BTT's power and flexibility.
I spent quite some time thinking I'd gotten things tangled up myself and thought it would be great to have a debug mode which shows what rules are being applied, in what order, to any given element. Not sure how difficult this would be (and I'm already coming up with some gotchas in my head), but fwiw, here's a feature request!