There is no need to change over from IRC source to the crystal source when running above 110MHz.
But normally there is a crystal, because of the higher accuracy, required for USB 2.0, for audio, etc. That's why there is this example in the user manual.
The IRC and the crystal are just 12MHz sources, that's the important information here. When the user manual says "run from the IRC" or "run from crystal" then this just means that the chip runs on a 12MHz clock. If you put the PLL in place, then the PLL is sourced from the 12MHz, but the chip (or part of the chip) runs on the PLL output clock.
Regards,
Bernhard.
