There are a few differences:

Yamaha presence speakers are placed higher and wider than the L/R mains. PLIIz recommends the height speakers be placed directly above the L/R mains.

Yamaha uses ambience generation, adding reverb and early reflections that weren't in the original recording. PLIIz is ambience extraction, using only information from the recording itself.

Yamaha's presence speakers are typically used for their room simulation DSP modes (to give the impression of being in a larges space). Some of these modes even have the names of the actual venues that Yamaha measured in order to generate the appropriate reverb.

By comparison, PLIIz only attempts to give a sense of height (z-axis), using decorrelated and non-directional information extracted from the surround channels. Think of it as taking a ring of sound and making it more of a bubble of sound.