am trying to use this to set some variable on button down/up state, however now the up button is taking over the normal click & basically rendering the left click unusable.
If you configure a trigger in BTT, the system will not perform the standard functionality anymore. You could of course try to send a left-mouse-down and left-mouse-up in your action sequence, but I would not recommend doing something like this. If you need to know whether a button is pressed, better use the variable "currently_pressed_mouse_buttons" which is also available as advanced trigger condition