Easy enough to science.
I spawned in 10 Mercury shuttles to my fleet, got into a battle, and threw them at the enemy 1 by 1.
Mercury 1-5 I piloted at the start or transferred into before they blew up.
Mercury 6-10 I left be unpiloted.
Then I nuked the enemy to win the battle.
Every Mercury I piloted was normally recoverable.
Every Mercury I didn't pilot was recoverable with a story point.
I repeated the test, but this time I hopped to every Mercury during the fight but left them all each before they were destroyed. So butt was in seat at some point, but not when ship go boom (except for ship #10, nowhere else to go). 3 ships were normally recoverable, 7 recoverable with story points.
1 final test, all 10 mercury sent in, none ever piloted. 3 normally recoverable, 7 recoverable with story points.
Conclusion:
Butt in seat when ship go boom, "officer" was present and you can recover normally.
Butt not in seat when ship go boom, it's like you were never there.