When following the instructions for Google Workspace, you can make the below adjustment to only archive select mailboxes if required.
G Suite setting to archive only specific mailboxes using the routing rule:
Please follow the steps provided in the instructions you received from MessageWatcher, then you can make an adjustment to select only specific mailboxes to be archived (by default the rule will archive all mailboxes).  In the Routing section you should see the rule for MessageWatcher.  This is the rule that determines what emails are archived. You can edit the rule and scroll to the bottom and select the “Use address lists to bypass or control application of this setting” option, and also select the “Only apply this setting for specific addresses/domains” option and enter your addresses that you would like to archive.

Finally save the rule.  Only the selected email accounts will now be archived.