The question of 'how do legit users use the matrix' is very much a "don't pay attention to the man behind the curtain" aspect of 5th edition rules. Because realistically:
GM: This host is very high security, hacking it will be difficult
Party: so, how does Jane Wageslave edit her files?
GM: Oh, legitimate users are different.
Face: OK, let's become a legitimate user, that sounds easier.
GM: Uh, you can't.
Face: We'll steal Jane's commlink and have her traquilized so she can't report it missing.
GM: Uh, it also uses biometrics ...
Face: No problem, I have the 'ware to copy her prints, eyes, and voice
GM: and, uh, she has to be at her desk to start the log-in
Mage: I can make the face look exactly like Jane
GM: well, there are also passwords
Party: (laughing) Oh, we can make her give us those, and have ways to make sure they are right.
GM: Ummm, ummmmm, uhhhh, that isn't how hacking works in Shadowrun though!
Seriously, as with our own times, social engineering probably should be the more powerful route to break into a system, with hacking being for when there just isn't time for that. But that would make decker and technos even more niche, so we sort of wave our hands and say that doesn't work, without ever explaining why it doesn't work.