I believe I have the resolution.
Since I had symlinked /opt/local/bin/clang-mp-13 to /usr/bin/clang, that is what occasioned the message that I needed to download and install Xcode's command line developer tools when I tried install.packages(...) the last time but one. However, the compilation still failed.
I saw that MacPorts had a clang-13 variant, so I tried to install that, but the installation failed because of my symlink in /opt/local/bin. I removed that and tried again, the install of clang-13 succeeded, produced a file /opt/local/bin/clang-mp-13.
I tried
install.packaged("ncdf4")
again, and it succeeded!
So, apparently, the clang version 13 that comes with Apple's Xcode doesn't work, but the one that comes with MacPorts does. The posted PDF says the same about Xcode 13.
Don't ask me why.