Tried X3 a bit, using the same clip as with X2 above. With NDME enabled:

1. As before, split a clip that had three notes near the split point, which was at a measure boundary. So two clips resulted, touching on one lane. I moved the 2nd clip down to another track for future reference. The two clips can be slipped to show all the notes from the original clip.
2. The clip has two notes that originally crossed the split boundary and a third that started on the split boundary. In the first clip of the split, the two notes appear truncated, the third one is no longer showing. The third note shows at the start of the 2nd split clip. (As in X2).
3. Quantized (the first clip) One of the two notes disappeared. Quantize would have moved it to the place where the clip ended, but the clip did not extend as it did in X2. This is acting like the project from the OP.
4. Then I slip-edited that clip to see what was left. some of the notes were still there, not quantized. However, two notes were missing: the one that got quantized out of the clip and the one that was formerly at the split boundary.

This is probably similar to what happened with the OP project.
 
Then I disabled NDME and started down the same path. The split extended the first part, and made overlapping clips, but did not create a 2nd lane. The OP project didn't seem to have the right lane structure either. Quantize did not extend the clip. One of the two notes appeared truncated, though its properties gave the original length. And slip editing revealed the rest of the note.
 
There are probably a lot of details I left out, but it's pretty clear there were major happenings from X2 to X3. There was a note disappearance in X2, but X3 seems not to make as much sense.
 
I became very curious about this after Dave's exhibit of X2 vs X3. I wondered what would happen to a non-destructively split-then-quantized clip when the clip lengthened and visible notes would be quantized to become aligned with, or overlap, invisible notes. Turns out, in X2 they deleted the invisible note that would have been exposed by the quantizing operation. In X3 they do clip lengthening differently, leave overlapping clips in one lane, and (some) formerly visible notes get deleted, not just made invisible.