There are a few possibilities.
Have you considered the XT250? I am not sure just how low you can make either of the XT but I am pretty sure it can be lowered at least an inch or two...which may help. Also look at the DR650, if you decide a 650 is what you'd like.
Cutting the seat down is an option but can compromise comfort if not done right. Try Custom boots with an inch added to the heal/soles. Don't go too thick or she won't wear them....unless you're going to a 70's Disco's
Yes, this really does help!!
The key thing here is your partner is going to have to learn to ride on tippy toes on a loaded bike at least some of the time. Even a 250 will get heavy when fully loaded. Much of this can be solved by the rider learning how to handle a heavy bike on tip toes or with only one foot down. Balance, practice,
and body position all play a part here.
Sounds daunting right? It's really not so bad but will require some practice and some strength training certainly would not hurt.
Start with the bike unloaded and go into the dirt and uneven ground. Teach her to turn round at slow speeds, figure of eights and such, (gently drag rear brake, steady throttle) Practice parking the bike, and mount and dismount. (always in horse style!). In a month or so she should see progress. Parking is where most shorties fall. She will need to learn how to position the bike correctly on uneven ground when parking even at weird angles (avoid them when you can).
Always make sure the side stand is not too long. After lowering the bike you will need to buy another stand or cut the stock one down. Not hard at all and a must to make the bike usable.
Technique while riding/parking is critical here. She can't expect to be sat in the middle of the seat, bolt upright, and get both feet flat, never happen. A shorty needs to use one bum cheek slid over onto to one side of the seat, and put (for example) the left foot down. (so you've got the right bum cheek on the left side of the seat, the left cheek is hangin off a bit and your left foot is on the floor) Clear as mud, right?
The right foot stays on the right peg, using the brake as needed. Also, its critical for her to slide ALL THE WAY forward on the seat. This reduces the distance from the seat to the ground. Get it? With practise all this get much easier, even with a loaded bike.
Getting back to bikes for a second....
She could also look into lowering something like the DRZ400S Suzuki. Problem here (and with other modern 400's) is they start off pretty tall (for off road capability) so getting them down really low is tough.
Also consider street bikes. Ninja 500 or 250, Suzuki GS500, Honda Rebel, or other of the multitude of lower seated, lightweight street bikes.
In the 650 single dual sport class there are certainly better choices than the F650 BMW, IMO. Not only is the F650 about 65 lbs. heavier than its competition, it is about double the price (as least here in the USA). Most of the dual sports are tall....with one exception.
The Suzuki DR650 is the ONLY dual sport 650 that is adjustable from the factory to be set lower. The rear shock has a two position adjuster to lower the bike by about 3/4". On the forks you simply turn over a spacer inside the fork to lower it 3/4" up front. All dealers know about this and its in the manual. Suzuki even make a shorter side stand for the lowered bike.
Want to go even lower? No problem!
Now, you can change the "Dog Bones" (shock links) to go down an additional inch or more at the rear! In the front you simply slide the fork tubes up in the triple clamps an inch (you can go TWO inches if you want!) So, now you are down nearly three inches from stock! And BTW, the DR is the lowest in class to start with. And remember, it's 65 lbs lighter than a BMW f650. 65 lbs. represents ALL your luggage and gear on a long trip. Weight is the enemy of the short of inseam.
A dealer friend (sells Honda, Suzuki and Kawi) has sort of become the short rider specialist in my area, selling brand new DR650's already lowered down. Several 5ft tall women have purchased these bikes and are very well pleased with them. A friend has one, now has 33,000 miles on it. She is 5'2".
You can get the Corbin seat which , if you scoot forward, makes it even easier for shorties to get both feet down with a 200% improvement in Bum
comfort. (I have one on my bike).
Sadly, apparently DR650's are not sold in the UK.