I think such a setup is not a mistake and must be allowed:
id col (default) - is default, not removable.
id col (user added) - for getting some resource-related data, based on resource id.
Ah.. I hurried too much to create an issue.
Render Snippet gets full information about the resource and [id] can be easily retrieved with
$modx->getOption('row', $scriptProperties, '')['id'];
I think such a setup is not a mistake and must be allowed: id col (default) - is default, not removable. id col (user added) - for getting some resource-related data, based on resource id.