Experience: Experience is treated way different in HOST and PHost.
Tim Continuum: When PHost detects that two players illegally share a registration number, their empire will stop working for a turn (ships do not move, planets do not produce). This makes it easier to continue the game after a Tim Continuum incident, because players do not get information they should not have (as it is the case in HOST which throws ships to random places). These days, most such incidents happen by accident, not by intention. In addition, PHost doesn't punish players for Red status TRNs. It just ignores the offending TRN files and continues as if the player had not submitted a turn file at all.
Ion Storms: Ion storms behave similar to those in HOST, but differ in details. Especially ship effects are computed differently, mainly because due to the different implementation of experience.