Configuration: PHost does not come with a "HConfig" program. Instead, PHost uses the plain-text file pconfig.src (and shiplist.txt) to define game parameters. Using the PControl feature, you can run add-ons at any place in the host sequence.
Data Files: PHost uses mostly the same file formats as HOST. It does not use all files HOST uses, and it uses some other ones. See the Technical Information page for more information.
AUXBATT.INI: PHost does not explicitly support the auxbatt.ini hook of HOST (this hook was present in older HOST versions, and went away without notice later). It does, however, support fine-grained hosting control which easily allows you to add it.
TacCom support: PHost does not support the sharing of alliance data in TRN files via the TacCom program. If PHost encounters a TRN file with alliance data in it (using the so-called "leech" method) then it will indicate that the TRN file is corrupt. There have been no requests so far to support TacCom, therefore there are no plans to add it.
Invocation: PHost supports a number of command line options which modify the behaviour. In particular, PHost can check TRN files for errors without actually doing a host run.
Compatibility: PHost is intended to be compatible to HOST, but can of course not be 100% identical. Some incompatible programs are listed in this FAQ entry.
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 or re-host the turn 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.