Why do motherboard voltages meet 5v standard when so much seems to work at 5.5?
Well, 5.5V (or 6V or 6.3V) are a common specifications for parts designed to work at 5V with a bit of tolerance. 5.5V for ICs is about as close as you want to call it (10% more than nominal). For example, the 74ACH00.
Often the 5V is biased a bit higher to account for conductor losses at full load, so you might find a regulated 5V wall wart that outputs 5.1V or even a bit higher with a light load.
You don't want the parts failing if things are just slightly off nominal. For example, the ubiquitous LM7805 regulator will output between 4.8 and 5.2V.