If you apply the same rate of taxes to all companies with the same revenue, regardless of their margins you have your choice of putting all low margin business out of business by assessing a tax higher than they can pay (to collect reasonable revenues from the high margin businesses), or leaving a lot of cash on the table in high margin industries (which as a tax authority you probably don't like).
Suppose there are two companies. The first company buys resource A for 100$ to produce B. The second company buys B for 110$ and produces C, which it sells to the public for 120$. A merger of both companies would approximately half their total revenue, but wouldn't change their total profit.
We don't want the tax system to determine the optimal size of a company.