The format of auxdata.hst has changed. Actually, that's the driving reason behind the new version number: doing new things in auxdata.hst means we need a new number, and to implement 999 ships and per-ship abilities, we need new auxdata things.
auxdata.hst is now divided into chunks, much like utilx.dat. This means it can now be extended without breaking existing programs. When you update a program for PHost 4, it will most likely work with everything that follows.