Towing: There are two towing models available in PHost. The AllowAlternativeTowing option chooses which one to use. The towing model decided under which condition a ship can tow another one which might not want to be towed.
Towing Cloaked Ships: In HOST, cloaking does not break a tow. In PHost, this can be configured with the AllowTowCloakedShips option.
The HOST behavior rationale is that allies should be able to tow each other's cloaked ships into combat. Unfortunately, it has the side effect of giving cloaking races little defense against the Privateers, since even if a towed ship cloaks, it will never escape the tow of a ship with gravitonic accelerators. A cheap Privateer gunboat can tow a cloaked ship to a starbase and just wait for its fuel to run out (due to cloak fuel burn) or its cloak to fail. The towed ship cannot escape.
PHost enables allies to tow each other's cloaked ships into combat, simply by having the allies give each other the Ship Level of alliance. Thus, there is really no need for non-allies to be able to tow cloaked ships, and the cloaking races can once again escape Privateer tows by cloaking. Thus, it is recommended that AllowTowCloakedShips be disabled.
Super Refit: Super Refit will not use parts which are allocated for a ship build order.
Colonization: When you scrap a ship using Colonize, you'll receive the minerals used to build the ship (multiplied by the RecycleRate), but no money. This differs somewhat from the HOST calculation. In particular, you'll not receive supplies for torps/fighters (i.e. the trick known as "Reverse Alchemy" does not work in PHost).
Pillage: When a ship pillages a planet in HOST, all other Klingon ships in orbit of the same planet will try to gather cash and supplies. Actually, it can even happen that the ship doing the Pillage will not get anything because it is preceded by many empty freighters. In PHost, only the ship with the Pillage mission will get the cash. It must be that way because otherwise Pillage would be pointless in a game with many Klingon players (PlayerSpecialMission configuration option). The CumulativePillaging option can compensate this difference a little and allow many ships to pillage and get stuff (but it will also let them all do damage).
HOST does an additional supply-repair stage after pillaging. PHost does not do that, thus ships cannot repair themselves using supplies gathered by Pillage.
