Hi,
if the trees have got some growing to do still (root stock wise doesn't matter if you limit the size above ground) then your right to be concerned about the effect they may have. This is what type2 stone is for rather than the usual type1 stone, it compacts less and will allow for more movement within the sub base (for you root growing space), if they haven't got any growing left to do or not much just type2 locally around the roots you expose, if lots type2 the lot will give a strong margin of error for your build.
Dean