You raise an interesting point - in fact, one hypothesis for burgeoning benefits offered to employees is that they hide your compensation in various tax-shielde

You raise an interesting point - in fact, one hypothesis for burgeoning benefits offered to employees is that they hide your compensation in various tax-shielded pots of money. From this perspective, the overhead costs of an employee and the tuition/facilities fees of PhD students are not so different from what happens in the working world. One large exception is the teaching function of PhD programs, which is often underwritten by outside funders (or by scholarships that students, themselves pursue). I'm not aware of a situation in which an employee would herself need to secure money to pay her overhead outside of academia. Thus, the comparison is a poor one - companies 'pay' you more by covering your overhead, but universities assess a tuition that is either paid by the student (e.g., in humanities) or by a funding organization (e.g., in the sciences).