The internal IDE controller can only access the first 4GB of a drive at boot time. If you have a 500GB drive fully working at boot time, then it is not connected to the internal IDE controller but to some third-party controller which supports large harddrives by firmware. Or you have a ROM expansion like Deneb, eFlash or Kickflash which contain the needed drivers.
Not to mention that there is no way to boot from PCMCIA without loading drivers first.
I had stated that I use the FastATA MKIII & the 4xEIDE boards in my A1200s, I didn't think that anyone would still be using a direct connection to the MB these days, it's way too slow that way for my liking...
Im not keen on those CF adapter things, I prefer to use USB and a multi card adapter...