Hi Bruce,
The native Logic instruments and effects are not available outside of the DAW, which is very similar to any DAW out there (Cubase, Live, ...).
AudioUnit and VST instruments are available directly in EigenD. There are several advantages to doing this:
1. you don't have to work with virtual MIDI interfaces to route data back and forth
2. you don't have a double latency (EigenD + DAW)
3. you can use host automation parameters directly and polyphonically (http://www.eigenlabs.com/wiki/2.0/Configuring_AudioUnit_and_VST_plugins/)
4. you can directly tie other controls like breath, strip, other keys, ... to your host parameters without having to convert to and from MIDI first
5. you can use the outgoing plugin audio directly in EigenD and route it back to the Eigenharp easily (Tau, Alpha) or process it further with other EigenD agents or other AU/VST plugins that can again be controlled directly by the Eigenharp
6. you're not limited to 7 bit MIDI resolution (very few DAWs actually properly support 14 bit MIDI)
7. you don't have to learn about the internal DAW routing, tracks, setup, switching, etc, etc
8. you don't deal with potential bugs of yet another software application
9. you use less resources both in RAM and CPU
10. for live usage it's much more trivial to have just one application to start to be able to play, as opposed to the right combination of a series of applications that have to work together
One thing to realize is that there's no reason to host an AU/VST inside your DAW just to be able to record MIDI. You can very well play a MIDI output at the same time as an AU instrument on the Eigenharp (select them both with the mode key) and you'll have all the benefits of both.
Finally, there's only one DAW that supports per-note high resolution expression editing, that's Cubase 6 with Note Expression. It's a premium feature on the full version of Cubase 6 and still requires you to use MIDI with voice-per-channel for polyphony to play the information in real time. There's no way yet to directly have it control VST3 note expression parameters that way though, that's only possible through polyphonic pressure at this time, but Steinberg might improve that for a next version.
Hope this helps,
Geert