The important thing to remember about LEDs is that you don't supply them with a recommended voltage like you do a light bulb - you supply them with recommended current
The easiest way of thinking about supplying an LED with power is to imagine the LED subtracting voltage from the circuit - the LED voltage drop.
Here's a simple problem:
You have a 5 V power supply, a red LED with 1.6 V drop[1], and a resistor. The recommended max current for the LED is 0.02 A.
The LED does not limit the current on its own. If you connect it direct to the power supply, it would be like connecting a short circuit across a (5-1.6 = 3.4 V) supply, and the LED would blow. You need the resistor to limit the current - in this case at least 3.4/0.02 = 170 ohms. This resistor is included on the motherboard.
Now, let's say you change the LED for a blue LED with a 3.5 V drop. The resistor is unchanged. What happens to the current? It will be considerably less than the original setup - sufficient to provide a reasonable light output but with no risk of burning out motherboard, or LED.
[1] LED voltage drop is dependant on colour. Red typically have the lowest at between 1.2-1.6. Green and yellow are slightly at 1.6 - 2.0 V. Blue (and white) are dramatically higher at between 3.4 - 4.0 V.