"whereas in PWM tone-duration pair form, one can use just two bytes to encode the same information, first being the tone frequence, and second being the duration (e.g. in seconds or 1/16th of seconds or similar)."
Maybe you don't understand what PWM is.
It does not allow you to define the tone (frequency), it allows you to define the ratio of the high part of the wave to the total wave. 100 means the high part will be 100/255 of the wave. The frequency is set at about 500hz.
Maybe you want to look at tone()