[noob]

Multiple rails started due to the ATX PSU specification stating that no output should provide more than 240VA, due to fire risks.

3.2.4. Power Limit / Hazardous Energy Levels

Under normal or overload conditions, no output shall continuously provide more than 240 VA under any conditions of load including output short circuit, per the requirement of UL 1950/ CSA 950/ EN 60950/ IEC 950.
—ATX12V Power Supply Design Guide, version 2.2

Thus having multiple rails on the 12V allowed a combined total of more than 240VA. And plugs were grouped for each rail to allow a spread of amperages accross them. Most of these PSU's though have a single high current source, and seperate regulators, and therefore the max total 12V draw is less than the combined max from each rail. More expensive (and the larger) PSU's are completly independent.

Most of the time the switch from multipe to a single rail, means that it is combining the regulators, and drawing current from them semi equally. The advantage of this, is if you have a single component that would normally draw more than the max amps off a single rail wont trip the PSU, but each regulator still conforms to the ATX specs.

The advantages of having multiple rails, is that you can not use 1 or more without having the same effect on efficiency as a single rail, and that the components for any single rail only have to meet a max of 20A for 12V, 48A for 5V and 72A for 3.3V, for which 5 and 3.3 V are typically much less than the max, allowing for smaller components.