The cable select functionality will still use a master/slave setup, but instead of a jumper, it's the connector of the IDE cable used which determines if the device should be master or slave (hence the name "cable select").
The problem is that cable select really isn't supported on the Amiga, and it will get confused if there are two devices attached to the IDE cable, where at least one of them is set up to be cs. Another type of device which have this kind of problems, is slimline IDE CD-ROM drives made in the later years.
My guess is that cable select is something that was added to the IDE standard some years after the A1200 was released.
And yes, setting up these type of cards can really be a PITA sometimes
