I will definitely update the deprecated calls. Of note, though, I think they are that way in the packaged examples.
As for the LED?
I’m feeling pretty draconian on this one. Pull the PWM capability out of the library - because a timer is a limited and valuable resource. If a project wants to dedicate a timer to the LED control, so be it, but that should not be permanently setup that way. Save the space and resources from the library and return it to project discretion.
Let setRGBled take on/off for each bit, using a color number (make it just setLed(); ). I know that gives you only eight colours and one of those is off. Use g-b-r to assign bits to the numbering so that 0,1,2,3 work everywhere, but 4,5,6,7 only work if you have a proper LED. The LED control byte in EEPROM is nothing more than a marker that says ‘switch the r/b bits’ on the way out to the port.
Push all the specialized stuff - PWM in particular (both for LED and sound) back into selectable libraries. That way, if a project wants the timers for a different purpose, there is a standard way to not attach them to LEDs and sounds.
I realize this is not the somewhat spiffy LED that was expected. But this is no longer a theoretical or design discussion. 80% of the Arduboys cannot light their green LED – and they are going to stay that way. Time to make the best of the hardware that is actually deployed.