Can my institution be a signatory to the V3.0 Indemnification but limit its scope, i.e. not apply it to a given study?

Yes, institutions which are both signatories to the V3.0 Indemnification Addendum can mutually agree to not apply the indemnification addendum to a specific study or specific body of research. This would require documentation of mutual agreement that both institutions have limited the scope to exclude the specific study in question.