So your theory is that this was completely coincidental. But after the voice was recorded, they thought, "Wow, it sounds just like the voice of the computer in Her! We should contact that actress and capitalize on it!"
That's what you're going with? It doesn't make sense, to me.
... that it would be even better to have a famous voice from Her than a rather generic female voice they had, but their proposal was declined. Well oops, but SJ, famous as she is, doesn't have a copyright right on all female voices other than her own.
Now listen to SJ's Samantha in Her and the first thing you'll notice are the voice breaks and that they break to a higher register with a distinct breathy sound, it's clearly falsetto. SJ seems to have this habit in her normal speaking voice as well but it's not as exaggerated and seems more accidental. Her voice is very much in her head or mask. The biggest commonality I can hear is that they both have a sibilant S and their regional accents are pretty close.