I didn't noticed any problems with that, which options you need to re-activate? These options seems to be active/changed in settings but are not working, or you can't set them permanently and each time you see default settings?
This script, like the previous one, is not using/hacking esc or search bar functionality in any way When you disable the script (in tampermonkey extension) esc is working? This would be totally weird
Let me now about any bugs, I'm using all functions and all is working for me, but it's still fresh so maybe there are some cases where it's more buggy
Agenda is on my todo list