Chrome External Protocol Policy

Since google considered the handling of External Protocols by external applications hazardous and it is no longer showing the checkbox with "Always open these types of links in the associated app"

This can only be enabled using a policy change.
In linux this is performed by adding a file.
Windows uses a registry entry and is not addressed here.

Add Chrome Policy File

As root create a directory /etc/opt/chrome/policies/managed

mkdir -p /etc/opt/chrome/policies/managed

Create an arbitrary named file using the default system editor.
In ths case the file is named external-protocol-checkbox.json.

editor /etc/opt/chrome/policies/managed/external-protocol-checkbox.json

Copy this Json content to the empty file.

Chrome version lower than 85.

{
    "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
}

Chrome version 85 or higher.

This allows all domains/origins from executing a magnet protocol link.

{
    "AutoLaunchProtocolsFromOrigins": [
        {
            "allowed_origins": ["*"],
            "protocol": "magnet"
        }
    ]
}

Check The Policy Change

Restart Chrome after the file has been added and open the policy using the local URL chrome://policy/.
Now the added entry should be visible.