Twice in irrops on split PNRs, my wife and I have been rebooked on different routings. When on the same PNR, this has never happened.

A single PNR also makes it easier to check itineraries as I only have to log in once.

And I've found that the act of splitting the PNR totally screws up upgrades and upgrade requests. On one trip, after the split, we ended up with nothing supporting two segments, and one segment had three upgrades devoted to it.