Answer
Not currently — IFS only provides the single user-level MSI variant; there's no separate admin/machine-level installer package available from IFS today. If the user-level native-messaging-hosts setting has to stay disabled for security-baseline reasons, the workaround is for the customer's own IT team to build their own custom install package (which won't carry IFS's own package signature, though the underlying executable inside it still will). Raising this as an improvement idea with IFS is the way to push for an official admin-installable package in the future.