Game mechanics aside, in Ilyana's case, it could be argued that she maybe "un-promoted" since she spent her time with the convoy guys traveling and not fighting, right? Jill, as far as I know, spent her time doing nothing until the Daein Liberation Army was formed. So maybe she "un-promoted" because she wasn't fighting before then. Or maybe she was? I mean, she would have to be doing something productive with her time; dragons don't feed themselves. Or maybe they do...? I think it would be more costly to feed Ilyana for three years than feeding a dragon for three years.
Mechanics-wise, they wanted to give you a strong mage and a strong flying unit during part 1, but they didn't want to make them crutch characters. In that dimension, I kinda wish they had just made two more new characters and had Ilyana and Jill rejoin at a later point. For example, maybe Jill was traveling with Haar and met up with Elincia and pals during part 2. And maybe Ilyana could have just stayed with the GM group instead. It woulda been nice to have met up with Melty the forgotten Pegasus Knight or something. Who knows?