Target Disk Mode uses the device specified by the "hd" devalias of the Open Firmware which defaults to the master on the (primary) IDE controller. Similarly the boot keys "c" (for starting from the optical drive), the eject key as well as the mouse button rely on the "cd" devalias to name the CD/DVD drive; therefore a Cube predefines this as the slave drive on the same cable as the hard drive (whereas most other Mac types use the master on the secondary IDE bus).
When both drive types get exchanged (HD addressed as slave and CD as master) the (contents of the) corresponding devaliases have to be redefined too using for example nvalias to store the new definitions permanently into the nvramrc to keep Target Disk Mode & friends working. This is of course optional as the Mac OS itself doesn't care about the devaliases.
Given the drives work together in this setup there will be no further need for the hardware modification of pin 28.