Most of the taxes a company actually pays are factored in with their workers' salaries. For example, if your company's average salary is lower to that of Apple for a comparable employee profile, you are effectively paying less taxes than Apple.

Or, if you company does not have profits, you are paying less taxes than a company that reports profits.

I do not think a company has to wear any nation flag. Companies have to care for their customers, employees and shareholders (in that order), wherever these are based.

Lawmakers need to care for their citizens, and need to legislate in a way that optimizes their tax collection in a sustainable way (i.e. lawmakers do not want companies or people fleeing to other countries or regions).

The resulting scenario is an optimal equilibrium of forces.