^^ I actually disagree because with 2 reservations you have other issues. They will not guarantee that you will not have to switch rooms, and you will have to pay two deposits and keep track of two reservations. (It also affects booking FPs and Dining). They really need to update their "systems" to accommodate things like this; it's not an unusual occurrence. Just one opinion, but other hotels we have stayed at have not made things so complicated.
Your information is slightly incorrect. I agree that WDW should have a better way to handle this, but I think 2 reservations is the better way to go.
We often do split stays, though we usually visit different resort. (We like the added variety of two different lounges, two pools, and varied park proximity.)
1. Keeping track of an additional reservation number is a non-issue, IMO. Two deposits yes, but no additional cost. Again, kind of a non-issue, IMO, unless they have cancel less than five days before arrival.
2. If they already made dining ADRs, there would be no change. They won't lose any ADRs they have. Otherwise, if we make our dining requests via IPO more than 180 days out, we've never had any trouble getting what we wanted (like BOG), and we also often do short stays. I also think if give IPO's both conf #'s, they might be able to make all their ADR's at once anyhow.
It would not affect their ability to book FP - EXCEPCT -
that they would now be able to book FP for everyone in their party at the 60 day window on the days that they have additional guests. That's what they would gain doing two reservations. The FP booking would be the same for the folks staying the entire time. They can book FP for both stays at the 60 window.
If they stay with one reservation, their two extra guests can't book FP at the 60 day window unless they pay the extra adult fee, $50, for every day of the hotel reservation.
If not, the additional guests would have to wait until the 30 day window to book FP. With two reservations, the folks staying the entire time can book all FP for the duration of both stays all at once. The additional guests can book at what will be
their 60 window.
Worst case scenario, is only that they'd have to swap rooms that day. For us, packing takes about 15 minutes.
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. 3rd floor is certainly a premier view. I just can't break away from the 1st floor cause we like to go right out onto the beach from our room. You know, our week there over July 4 was extremely hot too -- I think the hardest part was the heat index was usually right around 110 each day, temps in the upper 90's. And it didn't rain much at all! 
