Before I upgraded to the current version I was able to hold down a modifier key or a modifier key combo and just tap the stroke button without executing a gesture to triggers hotkeys I setup with Auto Hotkey.
I'm not sure what's changed in the new version but I was able to say, hold down Shift + Alt and tap the stroke button (MMB) and execute the hotkey I'd assigned to it. After reading the help file for advanced options I disabled the "Captured modifiers on stroke button down" and that helped some.