(Sorry for bumping an oldish thread, I found this when searching as I was wondering a similar thing when discussing this on another thread.)
The problem with the whole thing anyway is, from what I've gathered, that the AK package is a collection of freeware stuff so the "in part" thing is useless except, I guess, when talking about the installer. So, just strip the installer and install things manually and you're fine to take your emulated Amiga into battle. Wahoo!
Yes, this is the thing that I find more curious. You can put whatever terms you like on your own software (so it's fine for anything AmiKit specific like an installer or documentation), but it's less clear when it comes to compilations of software (e.g., some licences may disallow extra restrictions being placed on them, and surely you would be able to redistribute individual applications in the package, or some subset of the package).
Still, aside from this issue, AmiKit looks good.