Most of the JWP we see as bonsai are not from seed. They’re grafted. Of course, in Japan there are yamadori which are from seed, but by far the majority are grafted. A few are from cuttings or layers.
And, there is a reason for this. Most of the JWP from seed do not produce the tight, short bundle of needles that we (bonsaists) expect from JWP. You see, a few cultivars of dwarf mutations of JWP do produce those beautiful tufts of foliage, and the Japanese propagated them via grafts to make thousands of them. Older JWP with inferior foliage got grafted with the better foliage. So, JWP with the tight foliage are rare on their own roots.
They sew thousands of seed, grow them for a few years then cull out the ones with average to poor foliage. Keeping only a small percentage of the number sewn.
Any named cultivar is either a graft, or grown from a cutting or layer. A cultivar is a particular set of genetics. Anything from seed will have different genetics. Which is why growing JWP from seed, even from a cone from one of the desirable foliage types, will not give you seedlings with the same characteristics as the parent plant.