Battle order (numeric friendly codes) is now also considered for intercept attack. Previously, ships fought in decreasing Id order. This change is also available in PHost 3.4b.
PHost can now be configured so that colonists survive when a planet has been conquered in regular combat. After all, most of them are civilians. The ColonistCombatSurvivalRate specifies the percentage. However, colonists will get unhappier by ColonistCombatSurvivalRate / 2 points after combat. Because this option has the potential to severely change gameplay, it is only available in PHost 4.0 and later. (PHost 4.1d allows you to make this race-dependant upon both the captor and the captee, see option description.)
Ship list designers can now create Death Rays. Those ignore all shields and just kill crew. Hence, a death ray is well-suited for capturing enemy ships. A death ray is one having a "Bang" value of zero. The same goes for torpedoes.
Combat is affected by experience. Experienced ships fight better than inexperienced ones.
Otherwise, the battle mechanics did not change. When you use neither the Death Ray feature nor Experience, you can continue watching your combat using an older VCR player.