I'm not sure what "RCLONE_FILTER_FROM" does exactly as i can't find anything in the docs. But i assume this doesn't change anything regarding the priority of --include / --exclude / --filter. Which means RCLONE_FILTER_FROM won't work when also using --include.
I don't see why there would be any logic issues... it's just a matter of "include/exclude/filters" and "priority" of each rule.
But the way rclone works right now, it's simply not possible to "pin certain exclude rules as highest priority".
Anyways... i understand how it works now, thanks for all the info! 