It doesn't sound like she would be overbooted in any of the options you mentioned. If she is working on an axel now, then she could possibly be working on doubles before switching boots again. For all of the people I know who wear Jacksons, no one working on an axel is in anything lower than the Freestyle. The Freestyle, Elle, and Mystique are considered recreational boots and aren't meant to go much farther than the axel level. Not only are the boots not really made for it, but the included blades aren't, either.
We have (had? it's gone through a lot of changes) a local rental program. Most of the LTS kids go through the progression of Mystique to Freestyle. Those lower level Jacksons are likely rented and sold to recreational skaters all over the country. They are affordable and functional to get started, but they aren't really meant to take you into the competitive levels.
I would suggest looking outside the recreational line for axel and beyond. Even if it takes a few extra sessions to break in a stiffer boot, safety and injury prevention should be the main focus. As an aside, when I bought my last pair of boots, I tried on the Freestyle just to compare. I ended up buying a Jackson Premiere, but you wouldn't even know they were the same brand.
If your daughter is super concerned about break-in time, Edea Chorus boots are a possible solution. They are comparable to the lower level competitive Jackson boots but when punched and shaped properly require almost no painful break-in period.