OH, THE IRONY!
It must be WEIRD to experience a cutscene as the character in it.
And yes, of course she's wearing that. It's the default outfit when not wearing anything else.
What, she obviously wasn't wearing that under her outfit? Of course she wasn't! It's THE DEFAULT for when NOT WEARING ANYTHING ELSE. What part of this aren't you understanding?
In all seriousness, I don't this is handled that strangely in most games, as they're happy to put you in skimpy enough underpants and shirts that there's no lapse in logic.
Fallout 3 and New Vegas, meanwhile, insisted on shirts for men and women not wearing any armor, and it could get weird. A raider could be literally shirtless, or wearing some weird sort of sauce pan bikini top with nothing underneath, and they'd be wearing shirts after you looted them. It was all very odd.
This trend did not continue in Fallout 4, as literally everyone is wearing dirty white underwear, up to and including those in presumably sterile places with actual means of washing them. Yay...???