There is a patch-set for hdtoolboxes on the Aminet:
http://aminet.net/search.php?query=hdtoolboxIf I remember right, it requires some other software (program) that applies the patches to the HDToolbox files.
After that you don't see the disk is not type 7 announcement, and things should go as with hard disks normally.
Also, it might prevent some problems, if you set the MaxTransfer to 7E00, so the CF card will not get too large tranfer requests at once from the scsi.device ide-driver.
AFAIK some IDE devices misinterpret the sector count value, if it is not "modest" enough.