You are definitely not alone in this. I am facing the exact same audio issues on my Phone 3 too.
The normal call volume on the earpiece is surprisingly low. On top of that, I noticed that if the phone is even a little bit far away from my mouth, the mic does not pick up my voice clearly at all. Also, it feels like there is absolutely no native noise cancellation working during regular network calls.
Like you mentioned, since WhatsApp calls and media sound perfectly loud and clear, this definitely has to be a software tuning issue and not a hardware problem.
I am really hoping the Nothing development team takes note of this and rectifies these audio bugs in the upcoming April update. Fingers crossed!