I think the framing is a bit distorted in your representation of the situation. Pencil B provides more value to society as any of of these small companies can compete to do business with other entities while Pencil A can choose to avoid the overhead of establishing and maintaining these relationships, closing the market to small players that might seek to purchase graphite for other purposes, for example.

In an ideal situation Pencil B should be taxed less than Pencil A, as taxes would offset this overhead and incent this shift toward many small independent actors participating in an open marketplace.

In the real world, we have the opposite scenario. Companies are incentivized to become more like Pencil A, forming large vertical monopolies that minimize overhead and lock smaller players out. Even worse, once they're big enough to do business across national borders, taxation becomes mired in international law and cross-jurisdictional quagmires. In this laissez faire world, nations race to the bottom and compete for these businesses by offering places to incorporate at the lowest rates they can accommodate.