I think you are mistaken in your assumption here.
A remote will use the same settings for all sub-folders when you access it. The path you specify only determines what the root of that remote is.
So as long as you have a separate folder-structure for encrypted files - and another for unencrypted files then there should be no conflict.
Or are you saying that FreeNAS is doing encryption on it's own? That might certainly make problems as rclone could get confused seeing unrecognizable names. Why not just use rclone's encryption instead if that is the case?