There is no actual income being made. This is imposing a tax on something that no one actually gets! It's an accounting procedure used by Universities so they can meet the requirements of you being a student by law.
I am a PhD student. My tuition of $30,000/year is waived by the University of California since I take no classes and am purely doing research. I need to be a student for various tax purposes for both the University and myself. If the money from my waiver was taxed, I would somehow have to come up with an extra $10,000 out of nowhere! Where do I find that money? My PhD is my job. The government is not funding anything, and I feel you're using that terminology purely to muddy the issue.
To be clear, I don't much care for your argument here. Regardless of your ideological concerns about the ideal way to tax stuff, this policy clearly hurts people who are already in a precarious financial position. It will have remarkably negative effects for students like me. I will simply have to drop out, and all of the domestic PhD students I know in STEM will as well. We can't afford to take out loans for taxes...
This policy has a clear goal. It's impact is what matters. Simply demanding that the tax code be simplified is in this case ludicrous. You're really missing the forest for the trees here - this effectively kills all STEM PhDs in the United States. It's impact would be devastating.