SpamFilter has by default this filter disabled, as it can indeed cause false positives as you've noticed. Most of the issues are due to NDRs, even though there are a a few cases in which automated (valid) email notifications by companies could have an empty sender. This filter is an "all or nothing", so if you enable it, all emails with an empty MAIL FROM will be rejected - there is no way to pick and choose which ones are delivered and which are blocked, except by whitelisting senders.