Ryan, the answer to your "WHY?" is planned obsolescence. When you work inside the box, everything is easier and there's no MIDI sync nonsense, so they are "gently" pushing people to software synths.
However, there's a workaround that Akai MPC producers use to sync audio when tracking to DAWs:
Program a short percussive sound at the very beginning of each track where the sound doesn't start in the beginning of the first bar. Obviously it's not necessary for drums or other parts that start right away. If you want it to be absolutely perfect, move all your sequences a bit forward so that there's silence in the beginning, and put that percussive sound on every single track. When you track into Logic, you will see where exactly to align the multitrack.
If you are into MIDI, that is really easy and doesn't require figuring out how to sync through MIDI
PS: I am not sure if I understood correctly that you wanted to track in audio, but this would also work with MIDI tracks I suppose.
You should first look to correct the MIDI Buffer overflow problem, it sounds like a MIDI loop, this can be corrected in Logic.
The MIDI in clock sync has been removed on most Audio/MIDI sequencers mainly because of sync problems. Logic (and others) use the digital clock of the audio system to correctly sync MIDI and audio. MIDI (clock sync) resolution is 24 beats per quarter notes, audio resolution is whatever the sample rate selected, (say 44,100 samples per second). All modern DAW systems, at least the few I'm familiar with use audio clock, MIDI is synced to audio. The reason I mention all this is that MIDI clock is not professional quality sync, not only that... even with all of it's efficiency, Logic was never that great at stable MIDI clock lock, Logic 7 was the last version that could sync to MIDI clock and timing was starting to get iffy by then. Another reason is it allowed improvements to the audio engine that otherwise couldn't have been made. When Cubase adopted the Nuendo audio engine is when clock sync was removed, and that was before Logic had dropped MIDI clock sync.
Have you had a look at Reaper, I belive it locks to incoming MIDI clock.