1. That is the correct way to do it. If you do any input on the sticks while it is in a Virtual Stick flight it would also leave the programmed flight but then it will still need to change flight modes via the switch to be flown properly.
2. There is not. The newly upcoming versions 3 for Android (available via APK now) and 6 for iOS will have vertical mapping modes which will allow for what you are describing.
3. You need to wait for it to reconnect on its own before you hit reconnect. This is better on the new versions too.
4. If you don't let the aircraft come home on its own the waypoints will get out of sync. If the blue verification line shows it returning to the wrong abandonment point you can tap any corner waypoint to restart there so you don't have to refly too much.
https://support.dronesmadeeasy.com/hc/en-us/articles/115005940746-Manual-Restarting-Point