You are correct, that it doesn't make a difference, but you are not correct when you say that both drives will operate at ATA100 speeds. Modern IDE controllers support independent device timing. Each drive will operate at it's maximum speed.Doesn't make a difference. They will just operate at ATA100 speeds which isn't a big deal because no hard drive on the market can supply enough data to flood an ATA100 channel.
Modern IDE controllers support independent device timing. Each drive will operate at it's maximum speed.