In X1 I found that I could save even a large project while it was playing back and not cause a break in play. My current X2 test project always stalls for a fraction of a second when saving during playback.
If you have the time to strip down the project it would be interesting to know what aspect of the project causes this. I can't think of what change would have contributed to this off the top of my head. Regarding gaps while saving, with large projects personally I would prefer that the audio is stopped, but I do see the case of auto save etc where you might not want that. With large projects saving during playback actually slows down the save process since the processor is so busy. We in fact have an ini setting to temporarily stop playback and audio while saving...
BTW I missed another important optimization. Over the last few versions we have been continually updating our graphics engine and X2 has the most updates in this area. The graphics updates use more efficient drawing routines and offload more work to the GPU. Hence less kernel use and thereby less glitching at low latencies.