Actually, this is by design; when you click "Apply above settings to all hosts" check box, you intend to apply the settings for this host to all the other hosts.
You are right about the certificates, each scanner should have a separate certificate. Unfortunately, due to current design, if you choose to click "Apply above settings to all hosts" when separate certificates are enabled for different hosts, all hosts would get the same settings including the certificate setting from the host that you are currently editing.
As you pointed out, this configuration page needs some enhancement.
Regards,
Adnan