Thank you for citing IRS website, I looked at it and after the sentence you quoted there is another one:
"A student (including a trainee or business apprentice) or researcher who has become a resident alien for U.S. federal tax purposes may be able to claim benefits under a tax treaty that apply to reduce or eliminate U.S. federal tax on scholarship or fellowship grant income."
Here is a somwhat similar situation where resident alien was exempt from paying taxes (if I understood the thread correctly): https://ttlc.intuit.com/community/taxes/discussion/re-as-a-new-resident-alien-do-i-need-to-report-a-...
