1) There isn't a way to skip the Start/Stop Auto-Scroll layout action if an automation track is present. Automation tracks aren't just an alternative to automation tracks and can be used for other things, and can even be used to start and stop auto-scrolling. So the way to achieve what you're looking for is to remove the Start/Stop Auto-Scroll layout action and replace it with a Start/Stop Automation Track action. Then for each song where you want to use auto-scrolling, record an automation track that starts the auto-scrolling. Assuming you want to start the auto-scrolling at the start of these songs, you could then copy and paste that simple automation track to other songs.
2) Yes, if you have Settings > General Settings > Calculate Auto-Scroll Duration set to Manual, but you don't enter an Auto-Scroll Duration for a song, the auto-scroll function will use the regular Duration for a song. If that's not entered either, it will use the Default Song Duration for the set list (or Settings > General Settings > Defaults > Default Song Duration for smart lists). If that's not entered either, auto-scrolling won't start.
Maybe I should update the app so that if you enter a 0 into the manual Auto-Scroll Duration field, auto-scrolling won't start. Currently, a 0 is treated the same as an empty field, and would cause the function to look at the Duration and Default Song Duration.