Linking PNRs merely means that there's a note in the system that you are flying together but does nothing in terms of ensuring the passengers fly together in cases of interrupted flights.

We often have different means of payment when traveling as a family and so can't have the same PNR. I generally leave the upgrade requests in for all of us, but adjust seating on the day of the flight if a minor and parent aren't together in the same cabin.

On five years of domestic flights, I've never had Delta's system flag a small child flying on alone on his or her own PNR as possibly being unaccompanied.