Because there is no botpack in Unreal it was back-ported for compatibility use. There are several versions used in the Unreal servers depending on what you want to do. For instance I use a specific one in my server, different than the UT botpack.
That being said *NEVER* copy core files from one engine build to another. It's perfectly safe to use botpack.u like any other file in Unreal because it isn't a default file in that version. That's why it's tweaked and changed without creating problems. Only use the default botpack.u that is in the UT installation for any use in UT. I can't stress this enough: do not mix and match.