[zamfi]

I think the typical argument about tuition being an "accounting gimmick" is that it's the univerity paying itself for something -- does it actually come out of a budget, paid for by other students? (Unclear.) If there were no "tuition", would that money instead go to the student? (Unlikely.)

The question of whether senior doctoral students who aren't taking classes anymore should be paying tuition is a good one too! In the case described in the original article, though the student was in a masters program and quite likely taking classes—so not quite this scenario.

[Konnstann]

Anecdotal data from the grad programs in my area is that at least for PhD students your supervisor pays their tuition from whatever funding source they use to pay the stipend.

[zamfi]

Yes, and the supervisor also pays a fraction (often 50%+!) of any incoming grant money to “overhead” — to the institution, for lab space, staff, operations, etc.

Why some of this money is categorized as “tuition” and other money as “overhead” is at the root of the question I think.