Some things such as maples often will root at the union when is simply remains buried. This is unlikely with pines, generally speaking, though there are many known exceptions. On the other hand one may need to be concerned about roots being buried deeply enough to obscure the root stock - it very well be so deep as to cause root anoxia.
There are ways of obscuring the union, the simplest being the placement of some foliage across it in the field of view. Done well, on sees a fat nebari beneath the foliage and a thinner one emerging above that can impress as being trunk taper. Another is to create a shari across the union.
Put your mind to it and you'll likely come up with other ways to obscure the truth. This is much of the artistry of bonsai, IMHO.