I'm guessing this is an oversight on the devs part. To me it's a missed opportunity, these missions should have a permit supplied, you should be met by a guard at the pad, taken to the secure location for a hand-off and be met by a detail in the hangar to pass it off. But, I don't make this game.
I would absolutely
love to have missions where you could press E on a settlement worker to initiate some sort of dialogue - like having a guard escort you to a mission objective (and have the workers disregard your presence in restricted areas or other normally-illegal-but-mission-related activities as long as you're being escorted) or open a containment unit for the sample that you've been instructed to deliver, or whatever.
For extra fun, add some other mission wrinkles - you get escorted (or tailgate, or get given access as part of the mission) into the industrial production building and ask the worker there to open the sample containment without setting the alarm off. While the progress bar's ticking up, the alarm goes off for completely unrelated reasons and you hear gunfire as a dozen or so scavs are dumped into the settlement from a pair of dropships - all the settlement personnel immediately turn green if they're not already, whoever's nearest to you says something along the lines of "I hope you know how to use that gun!", and the new optional objective pops up - "repel the attackers". From that point on, none of the settlement personnel care about you having a gun out unless you use it on them specifically and you've got a choice - do you help and look to score some bounties, do you sit tight, grab what you came for and get out ASAP? Take advantage of the chaos to loot the place? Personally I think it'd be fun as
hell for a regular collection mission to turn into a pseudo-CZ.