It's not stealing though. The UI doesn't give you the theft warning when you take stuff from a restore/reactive mission. You are in fact legally entitled to take whatever you want, call it a bonus.
In some settlements, I need to call an Apex shuttle for free, hand off all the stuphz to the pilot, then get back to more looting. I rarely do it, though, because I get bored and also lose track of which buildings/rooms I already cleared out.