Your scenario makes sense, but it still doesn't cover empty areas once the show starts. If there is a line of disabled guests, sure, of course those spots are needed for them, but people have described the places being left empty when the show started.
Actually, if people are turned away from standing room only, and the accessible seats are still empty, then it is definitely an issue that WDW needs to address.
I think the reason they don't fill them is to avoid fights.
We saw a fight one time that nearly erupted into a fist fight. We were in the wheelchair spot almost as far over as you can get to the left of the theater. While we we sitting there, people kept coming from the standing room only area to sit there, despite the fact that they were still filling seats with guests with disabilities.
One family of about 5 in pafticular kept coming over and sat in the benches. Each time a CM brought another group to be seated, they told that family that they could not sit there. So, they were over numerous times.
There was another family with a small child who had asked early on if the mom and child could sit if there are were still seats left right before the show started.
When the CMs we done seating guests with disabilities and the show was about ready to start, there were 2 seats left and the CM supervising that area called over that woman and child to sit down.
When they came over, the family of 5 (plus some friends??) also came over and started yelling, "why does she get to sit there when you wouldn't let us?" there was yelling, swearing and some attempts to push from the family of 5.
The CM called a manger over and both told the family of 5 that they needed to Go back to the standing room area. The dad said they did not want to do that and they would stand behind us if they we not allowed to sit (kind of scary - I did not want them standing in back of us during the show). The CMs said they could not do that because they have to maintain an emergency aisle behind th seats during the show.
After a few minutes, they came to a truce, when the manager said either the people would go to the standing room only area or security would be called, the show would be delayed and they would be escorted out of the park.
This is probably more of a problem near the standing room only since there are many people there kind of waiting like vultures for a seat to empty in our experience. Away from that area, it's probably much less of a problem and we have seen CMs fill the seats right before the show starts.