Unfortunately, there is currently no way to set the Top Console User to Owned By for all Windows assets as a default.
Like you stated, this is currently a manual action as described here:
Lansweeper Classic links assets to other assets, such as Active Directory users, AD user groups, AD user OUs, and local Windows users. It also allows you to define the asset/asset or asset/user relationship, the relation start date and the relation end date. For instance, you can specify that asset A was borrowed by user X this month and that asset B is backed up to asset C. If a relation's end date is older than today, the asset or user page greys out the relation to show its expired status.
Read more here: Link assets to other assets or users - Lansweeper Community