Actually it's whatever that particular family wants to do, as there isn't anything wrong with going separate ways for a day if they WANT to. If it's better for them to split for a day, they should go for it.
The problem is that the family has NO idea IF they truly want to split up. They know nothing of the parks. The OP knows nothing of the parks. So it's a decision being made with absolutely no knowledge.
Since I have an older kid who can ride all the rides AND is still drawn to the kid areas, I know there are kid areas in both parks, and I know that my son would have had a blast at Universal, even before he could ride much at all. Of course, we weren't even going to WDW at that time, let alone Universal, so we never did it, but right now I can picture all of the little play areas that he would have spent the day in, if we had gone when he was little. Next time we go he'll be 10, and he's going to want to play in the Jurassic area (though now he's too tall to ride Pteranodon Flyers) and ride the carousel in Seuss and "red fish blue fish", and play in the Curious George area and the soft ball play area behind there, and play at the Fievel playground.... If we suddenly had a 3 year old I would take the 3 year old in a heartbeat.
But that's because I've been there and I know. My family has no problem splitting up for events, but that's once we KNOW what a place is like and if we like it or not.
I'll take them back when they are older, but even now at 7 & 11, I don't think it's worth it.
My nearly 10 year old would urge you to rethink.

He was 6.5 when we first went and even without riding any of the BIG rides he loved the place. Then he got brave enough for Forbidden Journey and it was all over. Now he can ride everything (though that's limited because I don't want him to ride alone, DH can't fit on the bigger rides, and I'm a chicken who has a limit on the terrifying rides I can do in a day or visit). And he's not even 10.
She just has to give me a definitive answer by 6/3 (dining reservation day) or it's counter service for them if they decide to stay at WDW with us
They can always cancel a reservation. They just have to do it the day before. If they end up with an extra table service credit I'm sure it can be fit in somewhere.