This adds an implicit --exclude * at the very end of the filter list. This means you can mix --include and --include-from with the other filters (eg --exclude) but you must include all the files you want in the include statement. If this doesn’t provide enough flexibility then you must use --filter-from.
So, because my --include-from has /DIR/** this overrides the --exclude?
My question becomes one of help! how do I order these right to get what I want? Is it even possible?
I think the solution you came up with is the best.
rclone is a little less flexible than rsync in that it doesn’t process the includes and excludes in the order of the command line - this is to do with the command line parser.
You could also write the --filter-from file as multiple --filter command line flags. I think the files is easier to maintain though.