Apply Custom email filters *before* Spam filter
I have 20+ filters set up for specific domains, showing that I clearly want/expect emails from them.
These emails should not end up in the Spam folder. I don't care what your 'statistical learning' thinks is spam. The defined filter clearly shows I WANT THE EMAIL. Your system should not override that.
The only exception I can think of would be if spam filter knows the email is dangerous. Not 'undesired' but destructive. In that case, perhaps overrule the Filter. But if the email is safe, my Filters should trump your statistics.
Alternatively (or in addition): Put a marker for the spam filter in the Filters list in the settings, so people can put filters both above and below it, thus showing which filters should apply before the Spam filter.