Add flag changes as a trigger for filters. For example when an email is marked as read, check if a filter is applicable and then process it. Other triggers could be applying a star or manually applying a label.

If the server load would be heavy, it could be set up as an up to 24-hours until the filter will apply to spread the load.

My pipe dream for my Proton (and work) mailbox is for all mail to land in my inbox and be filed away automatically into a folder after i read it