The master/slave configuration is used for parallel ATA drives using the older IDE interface. So if you want to plug two drives in IDE0 for example, one drive would be set to master and the other slave. However for PATA drives, if you have two and you also have two IDE interfaces, plug one onto IDE0 and the other in IDE1 both as master.
This config was common prior to SATA interfaces where you may have had multiple IDE devices including hard drives, and optical drives.
From my recollection and readings back in the days of computer repair, there is a disadvantage to running the master/slave configuration. While both drives are equal, in this configuration only one device can have access to the IDE channel at one time. The slave device gets to the channel through the master.
Other than that, I do not know of any other differences.
If I remember correctly, Master/Slave configuration is only available on IDE HDDs. They are not available on SATA Drives anymore. See Wiki excerpt below regarding the communication priority of Master/Slave HDDs on a single Parallel ATA port.
"Master and slave clarification
Although they are in extremely common use, the terms "master" and "slave" do not actually appear in current versions of the ATA specifications. The two devices are simply referred to as "device 0" and "device 1", respectively, in ATA-2 and later.
It is a common myth that the controller on the master drive assumes control over the slave drive, or that the master drive may claim priority of communication over the other device on the same ATA interface. In fact, the drivers in the host operating system perform the necessary arbitration and serialization, and each drive's onboard controller operates independently of the other."
Hmm... so all those times I ran MAster and slave on same channel instead of Master on separate channel I was actually hurting my speed.... Interesting. Still better than MFM.
I've learned back in the day and have always been under the assumption that only one drive can access the channel at a time. Makes sense. Of course the devices take turns. For that reason, I always separated each IDE device on its own channel.
I have not performed any benchmark tests though. I did not intend to indicate that the slave is dependent on the master, just in case that was inferred.