My only thought about this is that I heard that the scotch seed can stay dormant ready for germination for years, this is kind of like the mother nature knows best saying. If the scotch comes back then we know there is a problem that needs to be fixed. Is this a valid thought process?
Well, kinda. It's not always an indicator of poor soil either, I still have seedlings popping up in my fertile veggie patch. If new seedlings pop up, it's because there's enough light getting to the soil to trigger germination so in an orchard that could indicate a problem. Yes, the only thing that I've found that can choke it out is trees. However, it doesn't pop back from it's roots when you lop it off at the ground which is incredibly more wonderful than the blackberries which pop back as soon as you turn around. Once you get your clearing and planting done, it's not so hard to lop off the occasional seedling. As long as you get plenty of ground cover under your fruit trees, and you walk through with pruners on occasion, it shouldn't be too bad. Also, for what it's worth, my goats love scotch broom. It's all gone from their field so the stuff that pops up in other places I toss to them. I don't know if there's room in your plan for a livestock component, but it might be worth considering, though goats and fruit trees definitely don't mix.