Amorphs: Historically, PHost uses a different formula for Amorphous' colonist breakfast.

Unowned Planets: Even if a planet has mines and factories, these will not produce stuff when there are no colonists to operate them (i.e. the planet is unowned). Since there are not tax collectors, native taxes will be reset to 0. Natural processes like Trans-Uranium Decay and meteorites will still happen.

Overpopulation: Overpopulation is handled differently in PHost and HOST. The permitted population on each planet is computed differently, as are supplies eaten and climate deaths.

Meteor Effects: The exact happiness and population effects caused by a meteor in HOST are not known, so PHost has its own ranges.

New Natives: The exact ranges and probabilities for new natives in HOST are not known. PHost 4.0 has these configurable.

Siliconoids: In HOST, Siliconoid natives like it hot, like Crystals. In PHost, this is version-dependent:

This is a testing version.
It may be incomplete, and have more bugs (or features) than the public live version at planetscentral.com.