It's not so they can sit or stay together ON the bus it's so they can all be on the same bus, that's it. If able bodied people see they can't all get on the bus they can quickly decide to exit if they wish to wait for another bus. Not the same with disabled person in wc or ecv.
But that's not what the OP stated - he stated 'accompanying her on her seat', not that he wouldn't get on the bus. I took that to mean that the daughter was freaked that he wouldn't be right next to her. Many children have the same reaction, regardless of a disability.
I've been split from my family getting on buses - a few of us got on, some of us moved down the aisle a bit and got stuck back there, only to find out that the 2 family members behind me couldn't get on, the bus was full. (We love to do WDW with the inlaws!) The others couldn't get off, so our family was split. My daughters were very worried about Nana and Papa, as they had only been to WDW when it was the MK, many, many years ago. The girls thought Nana and Papa would get lost.