Historically, unions have been very antagonistic to capital. Paul Graham is basically the definition of capital; he uses his wealth to generate more wealth. And what he is suggesting is that startups could fix the inefficiencies in the market that unions have created. The problem is that fixing these inefficiencies would primarily benefit people like PG, who make their money from the ownership of enterprises rather than labor.
Generally speaking, the inefficiencies of unions exist to protect the interests of the workers, who generate wealth for the company but more often than not do not have an equity stake in the business. Unions exist to maintain the balance between capital and labor, and to make sure that people like PG don't deprive the laborers of fair remuneration for their work.
While we can almost always find someone who will do a job for less money, as a society we have an interest in providing an equitable share to labor, as there are far more workers driving this global economy than there are venture capitalists (or even just plain old capitalists) contributing to the economy in the form of seed round funding and the like.
Generally speaking, the inefficiencies of unions exist to protect the interests of the workers, who generate wealth for the company but more often than not do not have an equity stake in the business. Unions exist to maintain the balance between capital and labor, and to make sure that people like PG don't deprive the laborers of fair remuneration for their work.
While we can almost always find someone who will do a job for less money, as a society we have an interest in providing an equitable share to labor, as there are far more workers driving this global economy than there are venture capitalists (or even just plain old capitalists) contributing to the economy in the form of seed round funding and the like.