If you call Panam before the secret solo mission, she will be in your upgraded apartment at the end. She will still want to leave Night City, but you can tell her you have to do this one last thing, and she will understand.
You still get the "good" message from her at the end credits (where she says she will give you a long ride next time you see her), but not the "best" message you get from her in the Nomad ending.
I prefer the secret ending because Saul and Panam manage to work out their differences so it kind of sucks if Saul ends up dying. Plus you have to work a little harder for the secret ending, especially on Very Hard setting.