Ah, wait, I mis-looked, it is not the default config you try to do.
The default is exactly where you have it or you wouldn’t get the error message.
The default is gradle/libs.versions.toml.
If that file exists, a libs version catalog is created or if already present configured and the from call with the file is done.
If the file does not exist, then not.
So you have the file gradle/libs.versions.toml but try to configure libs.versions.toml which then fails due to calling from twice, once explicitly, once implicitly.
You can use the default file gradle/libs.versions.toml that already is present and remove your config.
You can remove that file and use a different location and configure it like you have it.
You can have both, but then use something different than libs for your additional version catalog.