Yeah, but this isn't necessarily about not trusting Windows apps, i.e. malice or malware, but rather that they can't be designed around it (since they assume Windows environment), so they would have privacy issues without even wanting to. At the very least maybe use `sd_id128_get_machine_app_specific` with a unique app ID for Wine? Simple and still better than nothing.
Otherwise, it would probably have to be done per-prefix (registry?), since two processes in the same prefix might want the same ID.