It's core 3.5, without pathfinder power creep in abilities. It was also before mounts were such customizable animal companions with just basic starting stat blocks. Mounted combat is a huge cluster f*** anyway. BTW - this isn't actually a rules question, because there's no doubt as to what it says. The question is why is it that way, what are reasonable houserules, etc.
If this is a home game, work with your DM (or player, depending on what side of the screen you are on) to resolve weirdness between:
trample feat by rider
trample special ability by mount
overrun
charge through
etc.
Almost nobody takes the trample feat anyway so I doubt adding one extra hoof attack is going to break much.
