Apparently, a software update has been released that fixes the CarPlay phone issue. I have a 2020 and have the same problem with Bluetooth working fine but terrible CarPlay phone quality.
Check this out:
2020 4Runner SR5P Carplay Issue | Page 5 | Toyota 4Runner Forum [4Runners.com]
According to at least one guy, the whole system becomes really sluggish when on a CarPlay call but I'll take it for now. Going to dealer ASAP to get the update.