Good questions!
Is there a way to have "start in air" selected by default?
I don't believe so, other than the checkbox before each mission.
is there a way to "Abort" a mission if you die so it doesn't kill your pilot when exiting, or to restart the same mission?
I think you have to select "pilot never dies" in Workshops to avoid dying. However, there is a way to refly a mission with a "dead" pilot,
if you use JJJ's Mission Editor. When you use the Mission Editor, it automatically saves your settings from the previous mission, so you can "resurrect" a deceased pilot. Download the ME and look over the readme file for more details.
Good luck!