It sounds like you want what has been discussed (but not yet implemented) here:
Since it sounds like you’re comfortable with run-script-before-required, until that feature is added I believe you CAN set a DUPLICATI__FILTER="-[Folder1]:-[Folder2]" environment variable which Duplicati SHOULD obey on startup.
Note that I haven’t actually tested this myself, so I could be wrong in the functionality OR the formatting.