If both the IDE driver and the file system support large harddrives, you can make partitions as big as you like.
As I said above, the driver of OS 3.1 can only see the first 4GB of the drive. 4GB of the drive, not 4GB partitions!! So on your CF with OS 3.1 you can use dh0, dh1 and dh2. With OS 3.9 you should be able to make an 8GB games partitions without problems.
In any case, do not use full format, always use quick. Never fully format a hard drive, it only produces hot air. Never ever fully format a flash memory storage, it significiantly reduces its live time and does nothing but produce hot air.
So out of interest why is full format available?