Just a quick update. While looking for solution to this problem, I have discovered much better way how to glue Finder and TotalFinder windows with regards to keyboard focus. This allowed me to remove tons of hacks previously I had to implement to emulate proper keyboard focus between Finder and TotalFinder windows.
In the next version 1.6.10, there will be this new system in place. It will lead to more stable and predictable TotalFinder behaviour.
Maybe this will introduce some other edge cases, but I’m pretty sure I will be able to fix them in next few releases. But great news is that this bug will be history!