In these cases, 'by' can be used but it changes what the speaker is expressing.
She won't be back until 5 o'clock.
expresses that Penelope will return at exactly 5 o'clock.
She won't be back by 5 o'clock
expresses that Penelope will return sometime after 5 o'clock. There is also an implication that something else will happen at 5 o'clock that Penelope will miss.
She won't be back until after 5 o'clock.
expresses that Penelope will return sometime after 5 o'clock, but nothing else is happening for Penelope to miss.
She will be back until 5 o'clock.
expresses that Penelope was away, then returned, is here now and will leave again at 5 o'clock.
She will be back by 5 o'clock.
expresses that Penelope will return sometime before 5 o'clock.