1. Core Audio is how Mac's natively handle all audio formats. It's designed to meet the requirements of the professional film and music industries. (Core Video).
http://developer.apple.com/technologies/mac/audio-and-video.html
This is available to professional downstream components using the FireWire out, or particular soundcards that are installed in workstation versions of the Macs.
2. I would strongly recommend finding a Mac mini, as you would probably find it limits the use of your MacBook Pro to just have it connected to your system, far away from you. The Mac mini can be placed inside a cabinet, and can then be controlled and updated using an iPad, a laptop, iPhone, etc. Screen Sharing on Macs lets you do most configuration and maintenance task as if you were controlling the Mini directly, over your network.
Some MacBook Pros do have FW out. You can pull an optical toslink signal to an Impact Twin, but then you might want to consider using a straight conversion, as originally proposed. The point is that your speakers are capable of such fine resolution that you want to ensure the best possible signal reaches them, and using FireWire out to a soundcard, and then going to your speakers, ensures that.
3. By direct connection I take it you mean taking a signal from the Minijack out from a Powerbook, and then going to AUX in on the BS3000 or 9000. I would be wary of damaging the speakers when inserting and removing the plug, unless the speakers are off. And you are then leaving the decoding of the audio signal to the cheaper DAC inside the Mac, which has been shown to be a very noisy environment as far as jitter is concerned. Stereophile/Cambridge Audio had a discussion about that which can be googled. Note that this discussion deals with USB out, which is much better than using Minijack out.
http://www.stereophile.com/content/cambridge-audio-azur-dacmagic-da-converter-manufacturers-comments
The mini is used for playback of a variety of video-files, including BD which has been extracted from the originals, using Plex which is multi-format capable. I send the audio for that to a surround processor, the pre-outs of which is connected to the LINE IN on the speakers.
Audio from the STB goes to the same surround processor via coax s/pdif, but can also be accessed directly through the Beomaster, when I only want 2-channel sound which is fed to the Beomaster via analog from the STB. That audio then reaches the BL5s through the Powerlink.