Background: I'm an EXP, (wife is AA Citi Card Holder), daughter has an Alaska Air Account

I booked LAX-PHX-LBB-PHX-LAX trip for this past weekend (paid ticket) in coach (not full Y). Travelling with 2 non-elite passengers (one of which is a 2 year old), I did not request an upgrade, and was perfectly fine sitting in Main Cabin Extra with my wife and daughter.

Check-In at LAX is fine, and we check 2 bags (one of which is 52 lbs or so)

Took First flight to PHX and went to Admirals Club for snack/rest etc. during layover. I get an alert on my phone from the AA App that my seat has been changed to 2F for my next flight.

I went to the AAngel in the club and she called down to the gate, and apparently the Gate Agent had like 8 open seats in F and began clearing ExPlats, Plats, and Full Y Fares into F, even if no upgrade was requested. I liked the sentiment, but was perfectly fine staying in coach with my wife and daughter. The gate agent, thankfully, was able to reverse the upgrade and put me back in my original MCE seat with family. No harm, no foul.

The only issue I saw was this: When the Gate Agent Processed my (unrequested) upgrade, it split my wife and daughter each onto a separate PNR. I now had 3 PNR's for our return journey rather than just 1.

For this trip, it didn't really matter, as I only had 2 bags for the 3 of us (though one was over 50lbs). But what would have happened if we had more than 4 bags on the return (my EXP free allowance, Plus my wife's 1 free bag for being a card holder)?

The rules specifically state that the companions need to be on the same PNR as the EXPlat to share in the increased baggage allowance. However, in this instance, my PNR was split into 3 (not at my direction).

Would I have been able to convince the Check-In Agent, or the AA computer system that we should actually have a 9 bag allowance (at up to 70 lbs each) instead of my 3 bag 70 lb allowance plus my wife's 1 bag 50 lb allowance and no allowance for my daughter?

Anyone else ever experienced this?