I see from the rsync man page that multiple --compare-dest directories are allowed there
Beginning in version 2.6.4, multiple --compare-dest directories
may be provided, which will cause rsync to search the list in
the order specified for an exact match. If a match is found
that differs only in attributes, a local copy is made and the
attributes updated. If a match is not found, a basis file from
one of the DIRs will be selected to try to speed up the transā
fer.
So maybe rclone should allow the flag to be repeated...