For conifers, you definitely want to keep the root ball as intact as possible. I don’t think that even with extreme care you can tease out individual roots without doing more harm than good. I agree that common juniper is damn hard to collect, but I wouldn’t say sylvestris is that difficult as long as you get a decent root ball collected. I’m a novice at collecting myself, but so far I’ve only managed to kill one sylvestris (that one I collected out of season, with little roots and minimal soil left around them, so it was a long shot to begin with).
I think your main problem is the area where you’re collecting. If your collecting in a place where the roots are free to grow far and wide they will. It’s only logical the tree tries to stretch its roots out as far as possible to guarantee its survival.
Apart from the harsh conditions in the mountains (or on top of rock) that stunt growth a major reason for collecting there is that trees grown in shallow soil pockets or cracks. When the tree only has a very limited area for root growth it makes collecting easier as you will find a solid root ball close to the trunk and in some cases there isn’t even a tap root as there’s no place for it to grow.
Close to my “hunting grounds” there’s an old sand/gravel pit with heaps of quite nice material, but I’ve never even attempted collecting there because I know the roots run for meters and meters and there’s no chance of getting enough root without excavating a several meter wide circle around the tree. And the soil is so loose that it would be almost impossible to get enough field soil to keep enough mycorrhiza for the tree to be healthy.
I’ve found a lot of really nice material that I just leave in the ground because I know it wouldn’t be responsible to try to collect it because of where it grows. I usually only look for yamadori material in places where I think collection is possible, for me, that’s on solid rock. And even then, I often found trees that can be collected. If, when I try to move a tree and it doesn’t budge at all, I know it grows down into a narrow crack and there’s no chance of getting enough roots to have it survive. Then I just leave it and keep searching.
I spend most of my yamadori hunting time on finding good material that can be collected with a high probability of success. Where I collect, a majority of the trees I find don’t fall into that category so I just enjoy them for a while and move on.