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Does AWS let you modify the main route table? Or does it only let you replace it with your own route table? I believe you can use

new aws.ec2.MainRouteTableAssociation

to replace the main route table with your own (with the tags you need). If you can modify it - then you may be able to

import

the automatically created route table and then add the desired tags to it. (though this would require a multi-step deployment).